Warning: Permanently added '13.222.144.201' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/9934621-rhel+epel-10-x86_64 --chroot rhel+epel-10-x86_64 Version: 1.6 PID: 8694 Logging PID: 8696 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 9934621, 'buildroot_pkgs': [], 'chroot': 'rhel+epel-10-x86_64', 'enable_net': True, 'fedora_review': False, 'git_hash': 'dbe5eefc32a1397ea896e140c921c6ffffc58ab9', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/orrisroot/el10/pymol', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'pymol', 'package_version': '3.1.0-13.1', 'project_dirname': 'el10', 'project_name': 'el10', 'project_owner': 'orrisroot', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/orrisroot/el10/rhel+epel-10-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'orrisroot/el10--orrisroot', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'orrisroot', 'tags': [], 'task_id': '9934621-rhel+epel-10-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/orrisroot/el10/pymol /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/orrisroot/el10/pymol', '/var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol'... Running: git checkout dbe5eefc32a1397ea896e140c921c6ffffc58ab9 -- cmd: ['git', 'checkout', 'dbe5eefc32a1397ea896e140c921c6ffffc58ab9', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol rc: 0 stdout: stderr: Note: switching to 'dbe5eefc32a1397ea896e140c921c6ffffc58ab9'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at dbe5eef automatic import of pymol Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading pymol-open-source-3.1.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o pymol-open-source-3.1.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/orrisroot/el10/pymol/pymol-open-source-3.1.0.tar.gz/md5/459f483231e1d521824b0e74df5ba640/pymol-open-source-3.1.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 28.1M 100 28.1M 0 0 452M 0 --:--:-- --:--:-- --:--:-- 454M INFO: Reading stdout from command: md5sum pymol-open-source-3.1.0.tar.gz INFO: Downloading pymol.png INFO: Calling: curl -H Pragma: -o pymol.png --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/orrisroot/el10/pymol/pymol.png/md5/3bbd85dbd40f588f505ad988b6df2933/pymol.png % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 19466 100 19466 0 0 1859k 0 --:--:-- --:--:-- --:--:-- 1900k INFO: Reading stdout from command: md5sum pymol.png tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1766135395.026526 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.13.7, NVR = mock-6.6-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1766135395.026526 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol/pymol.spec) Config(rhel+epel-10-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-10-x86_64-bootstrap-1766135395.026526/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.access.redhat.com/ubi10/ubi INFO: Pulling image: registry.access.redhat.com/ubi10/ubi INFO: Tagging container image as mock-bootstrap-ce444ada-52b1-4485-b848-a5e501700fbd INFO: Checking that df13daf315567aaa5c6e3045b9dc83cd99c670d64859eac902798d7a64187e75 image matches host's architecture INFO: Copy content of container df13daf315567aaa5c6e3045b9dc83cd99c670d64859eac902798d7a64187e75 to /var/lib/mock/rhel+epel-10-x86_64-bootstrap-1766135395.026526/root INFO: mounting df13daf315567aaa5c6e3045b9dc83cd99c670d64859eac902798d7a64187e75 with podman image mount INFO: image df13daf315567aaa5c6e3045b9dc83cd99c670d64859eac902798d7a64187e75 as /var/lib/containers/storage/overlay/6777cbb31cedaf51fcef3aaf5516d4ec3bada5f2317302c5d36efa36ecadcd33/merged INFO: umounting image df13daf315567aaa5c6e3045b9dc83cd99c670d64859eac902798d7a64187e75 (/var/lib/containers/storage/overlay/6777cbb31cedaf51fcef3aaf5516d4ec3bada5f2317302c5d36efa36ecadcd33/merged) with podman image umount INFO: Removing image mock-bootstrap-ce444ada-52b1-4485-b848-a5e501700fbd INFO: Package manager dnf4 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf4 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-20.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10_1.x86_64 python3-dnf-4.20.0-18.el10.noarch python3-dnf-plugins-core-4.7.0-9.el10.noarch yum-4.20.0-18.el10.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 3.3 kB/s | 1.8 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 170 MB/s | 40 MB 00:00 Red Hat Enterprise Linux 10 for x86_64 - AppStr 45 MB/s | 4.1 MB 00:00 Red Hat CodeReady Linux Builder for RHEL 10 x86 12 MB/s | 896 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 17 MB/s | 5.6 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash x86_64 5.2.26-6.el10 baseos 1.8 M bzip2 x86_64 1.0.8-25.el10 baseos 59 k coreutils x86_64 9.5-6.el10 baseos 1.1 M cpio x86_64 2.15-3.el10 baseos 296 k diffutils x86_64 3.10-8.el10 baseos 413 k epel-rpm-macros noarch 10-6.el10_1 epel 8.3 k findutils x86_64 1:4.10.0-5.el10 baseos 555 k gawk x86_64 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack x86_64 2.39-58.el10_1.2 baseos 45 k grep x86_64 3.11-10.el10 baseos 305 k gzip x86_64 1.13-3.el10 baseos 174 k info x86_64 7.1-6.el10 baseos 187 k patch x86_64 2.7.6-26.el10 appstream 134 k redhat-release x86_64 10.1-18.el10 baseos 61 k redhat-rpm-config noarch 293-1.el10 appstream 77 k rpm-build x86_64 4.19.1.1-20.el10 appstream 75 k sed x86_64 4.9-3.el10 baseos 322 k shadow-utils x86_64 2:4.15.0-8.el10 baseos 1.3 M tar x86_64 2:1.35-7.el10 baseos 866 k unzip x86_64 6.0-69.el10 baseos 190 k util-linux x86_64 2.40.2-13.el10 baseos 1.3 M which x86_64 2.21-44.el10_0 baseos 42 k xz x86_64 1:5.6.2-4.el10_0 baseos 481 k Installing dependencies: alternatives x86_64 1.30-2.el10 baseos 45 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs x86_64 4.0.3-4.el10 baseos 133 k authselect x86_64 1.5.0-8.el10 baseos 148 k authselect-libs x86_64 1.5.0-8.el10 baseos 227 k basesystem noarch 11-22.el10 baseos 8.3 k binutils x86_64 2.41-58.el10_1.2 baseos 6.4 M binutils-gold x86_64 2.41-58.el10_1.2 baseos 797 k bzip2-libs x86_64 1.0.8-25.el10 baseos 43 k ca-certificates noarch 2025.2.80_v9.0.305-102.el10_1 baseos 1.1 M coreutils-common x86_64 9.5-6.el10 baseos 2.2 M cracklib x86_64 2.9.11-8.el10 baseos 100 k cracklib-dicts x86_64 2.9.11-8.el10 baseos 3.7 M crypto-policies noarch 20250905-2.gitc7eb7b2.el10_1 baseos 98 k curl x86_64 8.12.1-2.el10 baseos 219 k cyrus-sasl-lib x86_64 2.1.28-29.el10 baseos 106 k debugedit x86_64 5.1-8.el10 appstream 80 k dwz x86_64 0.16-1.el10 appstream 140 k ed x86_64 1.20-5.el10 baseos 86 k efi-srpm-macros noarch 6-6.el10 appstream 25 k elfutils x86_64 0.193-1.el10 baseos 573 k elfutils-debuginfod-client x86_64 0.193-1.el10 baseos 47 k elfutils-default-yama-scope noarch 0.193-1.el10 baseos 13 k elfutils-libelf x86_64 0.193-1.el10 baseos 208 k elfutils-libs x86_64 0.193-1.el10 baseos 270 k file x86_64 5.45-8.el10 baseos 49 k file-libs x86_64 5.45-8.el10 baseos 764 k filesystem x86_64 3.18-17.el10 baseos 4.8 M fonts-srpm-macros noarch 1:2.0.5-18.el10 appstream 29 k forge-srpm-macros noarch 0.4.0-6.el10 appstream 23 k fpc-srpm-macros noarch 1.3-7.el10_1 epel 7.8 k gdb-minimal x86_64 16.3-2.el10 appstream 4.4 M gdbm x86_64 1:1.23-12.el10_0 baseos 156 k gdbm-libs x86_64 1:1.23-12.el10_0 baseos 60 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc x86_64 2.39-58.el10_1.2 baseos 2.1 M glibc-common x86_64 2.39-58.el10_1.2 baseos 339 k glibc-gconv-extra x86_64 2.39-58.el10_1.2 baseos 1.7 M gmp x86_64 1:6.2.1-12.el10 baseos 318 k go-srpm-macros noarch 3.6.0-4.el10 appstream 29 k jansson x86_64 2.14-3.el10 baseos 48 k json-c x86_64 0.18-3.el10 baseos 47 k kernel-srpm-macros noarch 1.0-25.el10 appstream 11 k keyutils-libs x86_64 1.6.3-5.el10 baseos 35 k krb5-libs x86_64 1.21.3-8.el10_0 baseos 767 k libacl x86_64 2.3.2-4.el10 baseos 27 k libarchive x86_64 3.7.7-4.el10_0 baseos 414 k libattr x86_64 2.5.2-5.el10 baseos 20 k libblkid x86_64 2.40.2-13.el10 baseos 124 k libbrotli x86_64 1.1.0-6.el10 baseos 349 k libcap x86_64 2.69-7.el10 baseos 95 k libcap-ng x86_64 0.8.4-6.el10 baseos 36 k libcom_err x86_64 1.47.1-4.el10 baseos 27 k libcurl x86_64 8.12.1-2.el10 baseos 371 k libeconf x86_64 0.6.2-4.el10 baseos 36 k libevent x86_64 2.1.12-16.el10 baseos 265 k libfdisk x86_64 2.40.2-13.el10 baseos 159 k libffi x86_64 3.4.4-10.el10 baseos 41 k libgcc x86_64 14.3.1-2.1.el10 baseos 145 k libgomp x86_64 14.3.1-2.1.el10 baseos 368 k libidn2 x86_64 2.3.7-3.el10 baseos 122 k libmount x86_64 2.40.2-13.el10 baseos 155 k libnghttp2 x86_64 1.64.0-2.el10 baseos 80 k libpkgconf x86_64 2.1.0-3.el10 baseos 41 k libpsl x86_64 0.21.5-6.el10 baseos 67 k libpwquality x86_64 1.4.5-12.el10 baseos 127 k libselinux x86_64 3.9-1.el10 baseos 97 k libsemanage x86_64 3.9-1.el10 baseos 122 k libsepol x86_64 3.9-1.el10 baseos 348 k libsmartcols x86_64 2.40.2-13.el10 baseos 83 k libssh x86_64 0.11.1-5.el10_1 baseos 233 k libssh-config noarch 0.11.1-5.el10_1 baseos 8.6 k libstdc++ x86_64 14.3.1-2.1.el10 baseos 924 k libtasn1 x86_64 4.20.0-1.el10 baseos 78 k libunistring x86_64 1.1-10.el10 baseos 550 k libutempter x86_64 1.2.1-15.el10 baseos 30 k libuuid x86_64 2.40.2-13.el10 baseos 28 k libverto x86_64 0.3.2-10.el10 baseos 24 k libxcrypt x86_64 4.4.36-10.el10 baseos 124 k libxml2 x86_64 2.12.5-9.el10_0 baseos 692 k libzstd x86_64 1.5.5-9.el10 baseos 294 k lua-libs x86_64 5.4.6-7.el10 baseos 134 k lua-srpm-macros noarch 1-15.el10 appstream 10 k lz4-libs x86_64 1.9.4-8.el10 baseos 70 k mpfr x86_64 4.2.1-5.el10 baseos 349 k ncurses-base noarch 6.4-14.20240127.el10 baseos 104 k ncurses-libs x86_64 6.4-14.20240127.el10 baseos 342 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 9.0 k openldap x86_64 2.6.9-1.el10 baseos 240 k openssl-fips-provider x86_64 3.0.7-8.el10 baseos 9.2 k openssl-fips-provider-so x86_64 3.0.7-8.el10 baseos 576 k openssl-libs x86_64 1:3.5.1-4.el10_1 baseos 2.3 M p11-kit x86_64 0.25.5-7.el10 baseos 501 k p11-kit-trust x86_64 0.25.5-7.el10 baseos 137 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 11 k pam x86_64 1.6.1-8.el10 baseos 586 k pam-libs x86_64 1.6.1-8.el10 baseos 58 k pcre2 x86_64 10.44-1.el10.3 baseos 250 k pcre2-syntax noarch 10.44-1.el10.3 baseos 155 k perl-srpm-macros noarch 1-57.el10 appstream 9.7 k pkgconf x86_64 2.1.0-3.el10 baseos 48 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config x86_64 2.1.0-3.el10 baseos 12 k popt x86_64 1.19-8.el10 baseos 70 k publicsuffix-list-dafsa noarch 20240107-5.el10 baseos 60 k pyproject-srpm-macros noarch 1.16.2-1.el10 appstream 16 k python-srpm-macros noarch 3.12-10.el10 appstream 24 k qt6-srpm-macros noarch 6.9.1-1.el10 appstream 11 k readline x86_64 8.2-11.el10 baseos 217 k rpm x86_64 4.19.1.1-20.el10 baseos 560 k rpm-build-libs x86_64 4.19.1.1-20.el10 baseos 93 k rpm-libs x86_64 4.19.1.1-20.el10 baseos 309 k rpm-sequoia x86_64 1.9.0.3-1.el10_1 baseos 968 k rust-toolset-srpm-macros noarch 1.88.0-1.el10 appstream 13 k setup noarch 2.14.5-7.el10 baseos 153 k sqlite-libs x86_64 3.46.1-5.el10_1 baseos 745 k systemd-libs x86_64 257-13.el10 baseos 823 k util-linux-core x86_64 2.40.2-13.el10 baseos 550 k xz-libs x86_64 1:5.6.2-4.el10_0 baseos 113 k zip x86_64 3.0-45.el10 baseos 270 k zlib-ng-compat x86_64 2.2.3-2.el10 baseos 79 k zstd x86_64 1.5.5-9.el10 baseos 468 k Transaction Summary ================================================================================ Install 146 Packages Total download size: 61 M Installed size: 187 M Downloading Packages: (1/146): authselect-libs-1.5.0-8.el10.x86_64.rp 5.2 MB/s | 227 kB 00:00 (2/146): authselect-1.5.0-8.el10.x86_64.rpm 2.8 MB/s | 148 kB 00:00 (3/146): basesystem-11-22.el10.noarch.rpm 503 kB/s | 8.3 kB 00:00 (4/146): alternatives-1.30-2.el10.x86_64.rpm 679 kB/s | 45 kB 00:00 (5/146): bash-5.2.26-6.el10.x86_64.rpm 91 MB/s | 1.8 MB 00:00 (6/146): bzip2-libs-1.0.8-25.el10.x86_64.rpm 1.2 MB/s | 43 kB 00:00 (7/146): bzip2-1.0.8-25.el10.x86_64.rpm 1.2 MB/s | 59 kB 00:00 (8/146): coreutils-9.5-6.el10.x86_64.rpm 26 MB/s | 1.1 MB 00:00 (9/146): cpio-2.15-3.el10.x86_64.rpm 14 MB/s | 296 kB 00:00 (10/146): cracklib-2.9.11-8.el10.x86_64.rpm 4.7 MB/s | 100 kB 00:00 (11/146): coreutils-common-9.5-6.el10.x86_64.rp 55 MB/s | 2.2 MB 00:00 (12/146): diffutils-3.10-8.el10.x86_64.rpm 28 MB/s | 413 kB 00:00 (13/146): ed-1.20-5.el10.x86_64.rpm 6.9 MB/s | 86 kB 00:00 (14/146): findutils-4.10.0-5.el10.x86_64.rpm 36 MB/s | 555 kB 00:00 (15/146): gawk-5.3.0-6.el10.x86_64.rpm 71 MB/s | 1.1 MB 00:00 (16/146): gdbm-1.23-12.el10_0.x86_64.rpm 13 MB/s | 156 kB 00:00 (17/146): gdbm-libs-1.23-12.el10_0.x86_64.rpm 4.9 MB/s | 60 kB 00:00 (18/146): grep-3.11-10.el10.x86_64.rpm 28 MB/s | 305 kB 00:00 (19/146): gzip-1.13-3.el10.x86_64.rpm 16 MB/s | 174 kB 00:00 (20/146): cracklib-dicts-2.9.11-8.el10.x86_64.r 49 MB/s | 3.7 MB 00:00 (21/146): jansson-2.14-3.el10.x86_64.rpm 3.3 MB/s | 48 kB 00:00 (22/146): json-c-0.18-3.el10.x86_64.rpm 2.7 MB/s | 47 kB 00:00 (23/146): libacl-2.3.2-4.el10.x86_64.rpm 2.2 MB/s | 27 kB 00:00 (24/146): libattr-2.5.2-5.el10.x86_64.rpm 907 kB/s | 20 kB 00:00 (25/146): libbrotli-1.1.0-6.el10.x86_64.rpm 25 MB/s | 349 kB 00:00 (26/146): info-7.1-6.el10.x86_64.rpm 2.1 MB/s | 187 kB 00:00 (27/146): libcap-2.69-7.el10.x86_64.rpm 8.4 MB/s | 95 kB 00:00 (28/146): keyutils-libs-1.6.3-5.el10.x86_64.rpm 429 kB/s | 35 kB 00:00 (29/146): libcap-ng-0.8.4-6.el10.x86_64.rpm 3.1 MB/s | 36 kB 00:00 (30/146): libeconf-0.6.2-4.el10.x86_64.rpm 2.8 MB/s | 36 kB 00:00 (31/146): libevent-2.1.12-16.el10.x86_64.rpm 23 MB/s | 265 kB 00:00 (32/146): libidn2-2.3.7-3.el10.x86_64.rpm 8.8 MB/s | 122 kB 00:00 (33/146): libnghttp2-1.64.0-2.el10.x86_64.rpm 7.4 MB/s | 80 kB 00:00 (34/146): libpsl-0.21.5-6.el10.x86_64.rpm 6.0 MB/s | 67 kB 00:00 (35/146): libpkgconf-2.1.0-3.el10.x86_64.rpm 1.8 MB/s | 41 kB 00:00 (36/146): libtasn1-4.20.0-1.el10.x86_64.rpm 7.1 MB/s | 78 kB 00:00 (37/146): libpwquality-1.4.5-12.el10.x86_64.rpm 5.4 MB/s | 127 kB 00:00 (38/146): libunistring-1.1-10.el10.x86_64.rpm 43 MB/s | 550 kB 00:00 (39/146): libverto-0.3.2-10.el10.x86_64.rpm 1.8 MB/s | 24 kB 00:00 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dwz-0.16-1.el10.x86_64.rpm 6.9 MB/s | 140 kB 00:00 (142/146): epel-rpm-macros-10-6.el10_1.noarch.r 4.6 MB/s | 8.3 kB 00:00 (143/146): ansible-srpm-macros-1-16.1.el10_0.no 1.9 MB/s | 20 kB 00:00 (144/146): fpc-srpm-macros-1.3-7.el10_1.noarch. 3.5 MB/s | 7.8 kB 00:00 (145/146): ghc-srpm-macros-1.9.2-1.el10_0.noarc 5.1 MB/s | 9.1 kB 00:00 (146/146): gdb-minimal-16.3-2.el10.x86_64.rpm 149 MB/s | 4.4 MB 00:00 -------------------------------------------------------------------------------- Total 44 MB/s | 61 MB 00:01 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 3.6 MB/s | 3.7 kB 00:00 Importing GPG key 0x5A6340B3: Userid : "Red Hat, Inc. (auxiliary key 3) " Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat10-release Key imported successfully Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat10-release Key imported successfully Extra Packages for Enterprise Linux 10 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xE37ED158: Userid : "Fedora (epel10) " Fingerprint: 7D8D 15CB FC4E 6268 8591 FB26 33D9 8517 E37E D158 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-10 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-17.el10.x86_64 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-2.1.el10.x86_64 1/146 Running scriptlet: libgcc-14.3.1-2.1.el10.x86_64 1/146 Installing : redhat-release-10.1-18.el10.x86_64 2/146 Installing : setup-2.14.5-7.el10.noarch 3/146 Running scriptlet: setup-2.14.5-7.el10.noarch 3/146 Installing : filesystem-3.18-17.el10.x86_64 4/146 Installing : basesystem-11-22.el10.noarch 5/146 Installing : ghc-srpm-macros-1.9.2-1.el10_0.noarch 6/146 Installing : fpc-srpm-macros-1.3-7.el10_1.noarch 7/146 Installing : ansible-srpm-macros-1-16.1.el10_0.noarch 8/146 Installing : rust-toolset-srpm-macros-1.88.0-1.el10.noarch 9/146 Installing : qt6-srpm-macros-6.9.1-1.el10.noarch 10/146 Installing : kernel-srpm-macros-1.0-25.el10.noarch 11/146 Installing : openblas-srpm-macros-2-19.el10.noarch 12/146 Installing : ocaml-srpm-macros-10-4.el10.noarch 13/146 Installing : package-notes-srpm-macros-0.5-13.el10.noarch 14/146 Installing : 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bzip2-libs-1.0.8-25.el10.x86_64 28/146 Installing : xz-libs-1:5.6.2-4.el10_0.x86_64 29/146 Installing : popt-1.19-8.el10.x86_64 30/146 Installing : readline-8.2-11.el10.x86_64 31/146 Installing : libstdc++-14.3.1-2.1.el10.x86_64 32/146 Installing : libuuid-2.40.2-13.el10.x86_64 33/146 Installing : libblkid-2.40.2-13.el10.x86_64 34/146 Installing : libattr-2.5.2-5.el10.x86_64 35/146 Installing : libacl-2.3.2-4.el10.x86_64 36/146 Installing : libxcrypt-4.4.36-10.el10.x86_64 37/146 Installing : libzstd-1.5.5-9.el10.x86_64 38/146 Installing : elfutils-libelf-0.193-1.el10.x86_64 39/146 Installing : gmp-1:6.2.1-12.el10.x86_64 40/146 Installing : gdbm-libs-1:1.23-12.el10_0.x86_64 41/146 Installing : libeconf-0.6.2-4.el10.x86_64 42/146 Running scriptlet: crypto-policies-20250905-2.gitc7eb7b2.el10_1.noa 43/146 Installing : crypto-policies-20250905-2.gitc7eb7b2.el10_1.noa 43/146 Running scriptlet: crypto-policies-20250905-2.gitc7eb7b2.el10_1.noa 43/146 Installing : mpfr-4.2.1-5.el10.x86_64 44/146 Installing : gawk-5.3.0-6.el10.x86_64 45/146 Installing : dwz-0.16-1.el10.x86_64 46/146 Installing : unzip-6.0-69.el10.x86_64 47/146 Installing : file-libs-5.45-8.el10.x86_64 48/146 Installing : file-5.45-8.el10.x86_64 49/146 Installing : alternatives-1.30-2.el10.x86_64 50/146 Installing : jansson-2.14-3.el10.x86_64 51/146 Installing : libcap-ng-0.8.4-6.el10.x86_64 52/146 Installing : audit-libs-4.0.3-4.el10.x86_64 53/146 Installing : pam-libs-1.6.1-8.el10.x86_64 54/146 Installing : libcap-2.69-7.el10.x86_64 55/146 Installing : systemd-libs-257-13.el10.x86_64 56/146 Installing : libtasn1-4.20.0-1.el10.x86_64 57/146 Installing : libunistring-1.1-10.el10.x86_64 58/146 Installing : libidn2-2.3.7-3.el10.x86_64 59/146 Installing : lua-libs-5.4.6-7.el10.x86_64 60/146 Installing : lz4-libs-1.9.4-8.el10.x86_64 61/146 Installing : pcre2-10.44-1.el10.3.x86_64 62/146 Installing : grep-3.11-10.el10.x86_64 63/146 Installing : xz-1:5.6.2-4.el10_0.x86_64 64/146 Installing : libffi-3.4.4-10.el10.x86_64 65/146 Installing : libsepol-3.9-1.el10.x86_64 66/146 Installing : libselinux-3.9-1.el10.x86_64 67/146 Installing : sed-4.9-3.el10.x86_64 68/146 Installing : findutils-1:4.10.0-5.el10.x86_64 69/146 Installing : libmount-2.40.2-13.el10.x86_64 70/146 Installing : libsmartcols-2.40.2-13.el10.x86_64 71/146 Installing : util-linux-core-2.40.2-13.el10.x86_64 72/146 Installing : tar-2:1.35-7.el10.x86_64 73/146 Installing : libsemanage-3.9-1.el10.x86_64 74/146 Installing : shadow-utils-2:4.15.0-8.el10.x86_64 75/146 Running scriptlet: libutempter-1.2.1-15.el10.x86_64 76/146 Installing : libutempter-1.2.1-15.el10.x86_64 76/146 Installing : p11-kit-0.25.5-7.el10.x86_64 77/146 Installing : p11-kit-trust-0.25.5-7.el10.x86_64 78/146 Running scriptlet: p11-kit-trust-0.25.5-7.el10.x86_64 78/146 Installing : zstd-1.5.5-9.el10.x86_64 79/146 Installing : libpsl-0.21.5-6.el10.x86_64 80/146 Installing : zip-3.0-45.el10.x86_64 81/146 Installing : gdbm-1:1.23-12.el10_0.x86_64 82/146 Installing : cyrus-sasl-lib-2.1.28-29.el10.x86_64 83/146 Installing : libfdisk-2.40.2-13.el10.x86_64 84/146 Installing : libxml2-2.12.5-9.el10_0.x86_64 85/146 Installing : bzip2-1.0.8-25.el10.x86_64 86/146 Installing : sqlite-libs-3.46.1-5.el10_1.x86_64 87/146 Installing : cpio-2.15-3.el10.x86_64 88/146 Installing : diffutils-3.10-8.el10.x86_64 89/146 Installing : ed-1.20-5.el10.x86_64 90/146 Installing : patch-2.7.6-26.el10.x86_64 91/146 Installing : json-c-0.18-3.el10.x86_64 92/146 Installing : keyutils-libs-1.6.3-5.el10.x86_64 93/146 Installing : libbrotli-1.1.0-6.el10.x86_64 94/146 Installing : libnghttp2-1.64.0-2.el10.x86_64 95/146 Installing : libpkgconf-2.1.0-3.el10.x86_64 96/146 Installing : pkgconf-2.1.0-3.el10.x86_64 97/146 Installing : pkgconf-pkg-config-2.1.0-3.el10.x86_64 98/146 Installing : libverto-0.3.2-10.el10.x86_64 99/146 Installing : libcom_err-1.47.1-4.el10.x86_64 100/146 Installing : libgomp-14.3.1-2.1.el10.x86_64 101/146 Installing : elfutils-default-yama-scope-0.193-1.el10.noarch 102/146 Running scriptlet: elfutils-default-yama-scope-0.193-1.el10.noarch 102/146 Installing : coreutils-common-9.5-6.el10.x86_64 103/146 Installing : openssl-fips-provider-so-3.0.7-8.el10.x86_64 104/146 Installing : openssl-fips-provider-3.0.7-8.el10.x86_64 105/146 Installing : openssl-libs-1:3.5.1-4.el10_1.x86_64 106/146 Installing : coreutils-9.5-6.el10.x86_64 107/146 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10_1.no 108/146 Installing : ca-certificates-2025.2.80_v9.0.305-102.el10_1.no 108/146 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10_1.no 108/146 Installing : authselect-libs-1.5.0-8.el10.x86_64 109/146 Installing : gzip-1.13-3.el10.x86_64 110/146 Installing : cracklib-2.9.11-8.el10.x86_64 111/146 Installing : krb5-libs-1.21.3-8.el10_0.x86_64 112/146 Installing : libarchive-3.7.7-4.el10_0.x86_64 113/146 Installing : libssh-0.11.1-5.el10_1.x86_64 114/146 Installing : cracklib-dicts-2.9.11-8.el10.x86_64 115/146 Installing : libpwquality-1.4.5-12.el10.x86_64 116/146 Installing : pam-1.6.1-8.el10.x86_64 117/146 Installing : libevent-2.1.12-16.el10.x86_64 118/146 Installing : openldap-2.6.9-1.el10.x86_64 119/146 Installing : libcurl-8.12.1-2.el10.x86_64 120/146 Installing : elfutils-libs-0.193-1.el10.x86_64 121/146 Installing : elfutils-debuginfod-client-0.193-1.el10.x86_64 122/146 Installing : binutils-gold-2.41-58.el10_1.2.x86_64 123/146 Running scriptlet: binutils-gold-2.41-58.el10_1.2.x86_64 123/146 Installing : binutils-2.41-58.el10_1.2.x86_64 124/146 Running scriptlet: binutils-2.41-58.el10_1.2.x86_64 124/146 Installing : elfutils-0.193-1.el10.x86_64 125/146 Installing : gdb-minimal-16.3-2.el10.x86_64 126/146 Installing : debugedit-5.1-8.el10.x86_64 127/146 Installing : curl-8.12.1-2.el10.x86_64 128/146 Installing : rpm-sequoia-1.9.0.3-1.el10_1.x86_64 129/146 Installing : rpm-libs-4.19.1.1-20.el10.x86_64 130/146 Running scriptlet: rpm-4.19.1.1-20.el10.x86_64 131/146 Installing : rpm-4.19.1.1-20.el10.x86_64 131/146 Installing : efi-srpm-macros-6-6.el10.noarch 132/146 Installing : lua-srpm-macros-1-15.el10.noarch 133/146 Installing : rpm-build-libs-4.19.1.1-20.el10.x86_64 134/146 Installing : go-srpm-macros-3.6.0-4.el10.noarch 135/146 Installing : fonts-srpm-macros-1:2.0.5-18.el10.noarch 136/146 Installing : forge-srpm-macros-0.4.0-6.el10.noarch 137/146 Installing : python-srpm-macros-3.12-10.el10.noarch 138/146 Installing : redhat-rpm-config-293-1.el10.noarch 139/146 Installing : rpm-build-4.19.1.1-20.el10.x86_64 140/146 Installing : pyproject-srpm-macros-1.16.2-1.el10.noarch 141/146 Installing : util-linux-2.40.2-13.el10.x86_64 142/146 Running scriptlet: util-linux-2.40.2-13.el10.x86_64 142/146 Installing : authselect-1.5.0-8.el10.x86_64 143/146 Installing : which-2.21-44.el10_0.x86_64 144/146 Installing : info-7.1-6.el10.x86_64 145/146 Installing : epel-rpm-macros-10-6.el10_1.noarch 146/146 Running scriptlet: filesystem-3.18-17.el10.x86_64 146/146 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10_1.no 146/146 Running scriptlet: authselect-libs-1.5.0-8.el10.x86_64 146/146 Running scriptlet: rpm-4.19.1.1-20.el10.x86_64 146/146 Running scriptlet: epel-rpm-macros-10-6.el10_1.noarch 146/146 Installed products updated. Installed: alternatives-1.30-2.el10.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-4.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-58.el10_1.2.x86_64 binutils-gold-2.41-58.el10_1.2.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 ca-certificates-2025.2.80_v9.0.305-102.el10_1.noarch coreutils-9.5-6.el10.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20250905-2.gitc7eb7b2.el10_1.noarch curl-8.12.1-2.el10.x86_64 cyrus-sasl-lib-2.1.28-29.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.193-1.el10.x86_64 elfutils-debuginfod-client-0.193-1.el10.x86_64 elfutils-default-yama-scope-0.193-1.el10.noarch elfutils-libelf-0.193-1.el10.x86_64 elfutils-libs-0.193-1.el10.x86_64 epel-rpm-macros-10-6.el10_1.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-1:4.10.0-5.el10.x86_64 fonts-srpm-macros-1:2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1:1.23-12.el10_0.x86_64 gdbm-libs-1:1.23-12.el10_0.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-58.el10_1.2.x86_64 glibc-common-2.39-58.el10_1.2.x86_64 glibc-gconv-extra-2.39-58.el10_1.2.x86_64 glibc-minimal-langpack-2.39-58.el10_1.2.x86_64 gmp-1:6.2.1-12.el10.x86_64 go-srpm-macros-3.6.0-4.el10.noarch grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-25.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10_0.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10_0.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-6.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-4.el10.x86_64 libcurl-8.12.1-2.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-2.1.el10.x86_64 libgomp-14.3.1-2.1.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-1.el10.x86_64 libsemanage-3.9-1.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-5.el10_1.x86_64 libssh-config-0.11.1-5.el10_1.noarch libstdc++-14.3.1-2.1.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10_0.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-5.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.9-1.el10.x86_64 openssl-fips-provider-3.0.7-8.el10.x86_64 openssl-fips-provider-so-3.0.7-8.el10.x86_64 openssl-libs-1:3.5.1-4.el10_1.x86_64 p11-kit-0.25.5-7.el10.x86_64 p11-kit-trust-0.25.5-7.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-8.el10.x86_64 pam-libs-1.6.1-8.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.16.2-1.el10.noarch python-srpm-macros-3.12-10.el10.noarch qt6-srpm-macros-6.9.1-1.el10.noarch readline-8.2-11.el10.x86_64 redhat-release-10.1-18.el10.x86_64 redhat-rpm-config-293-1.el10.noarch rpm-4.19.1.1-20.el10.x86_64 rpm-build-4.19.1.1-20.el10.x86_64 rpm-build-libs-4.19.1.1-20.el10.x86_64 rpm-libs-4.19.1.1-20.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10_1.x86_64 rust-toolset-srpm-macros-1.88.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-8.el10.x86_64 sqlite-libs-3.46.1-5.el10_1.x86_64 systemd-libs-257-13.el10.x86_64 tar-2:1.35-7.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10_0.x86_64 xz-1:5.6.2-4.el10_0.x86_64 xz-libs-1:5.6.2-4.el10_0.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-2.el10.x86_64 zstd-1.5.5-9.el10.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.30-2.el10.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-4.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-58.el10_1.2.x86_64 binutils-gold-2.41-58.el10_1.2.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 ca-certificates-2025.2.80_v9.0.305-102.el10_1.noarch coreutils-9.5-6.el10.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20250905-2.gitc7eb7b2.el10_1.noarch curl-8.12.1-2.el10.x86_64 cyrus-sasl-lib-2.1.28-29.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.193-1.el10.x86_64 elfutils-debuginfod-client-0.193-1.el10.x86_64 elfutils-default-yama-scope-0.193-1.el10.noarch elfutils-libelf-0.193-1.el10.x86_64 elfutils-libs-0.193-1.el10.x86_64 epel-rpm-macros-10-6.el10_1.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-4.10.0-5.el10.x86_64 fonts-srpm-macros-2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1.23-12.el10_0.x86_64 gdbm-libs-1.23-12.el10_0.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-58.el10_1.2.x86_64 glibc-common-2.39-58.el10_1.2.x86_64 glibc-gconv-extra-2.39-58.el10_1.2.x86_64 glibc-minimal-langpack-2.39-58.el10_1.2.x86_64 gmp-6.2.1-12.el10.x86_64 go-srpm-macros-3.6.0-4.el10.noarch gpg-pubkey-5a6340b3-6229229e gpg-pubkey-e37ed158-65785fa9 gpg-pubkey-fd431d51-4ae0493b grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-25.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10_0.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10_0.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-6.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-4.el10.x86_64 libcurl-8.12.1-2.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-2.1.el10.x86_64 libgomp-14.3.1-2.1.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-1.el10.x86_64 libsemanage-3.9-1.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-5.el10_1.x86_64 libssh-config-0.11.1-5.el10_1.noarch libstdc++-14.3.1-2.1.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10_0.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-5.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.9-1.el10.x86_64 openssl-fips-provider-3.0.7-8.el10.x86_64 openssl-fips-provider-so-3.0.7-8.el10.x86_64 openssl-libs-3.5.1-4.el10_1.x86_64 p11-kit-0.25.5-7.el10.x86_64 p11-kit-trust-0.25.5-7.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-8.el10.x86_64 pam-libs-1.6.1-8.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.16.2-1.el10.noarch python-srpm-macros-3.12-10.el10.noarch qt6-srpm-macros-6.9.1-1.el10.noarch readline-8.2-11.el10.x86_64 redhat-release-10.1-18.el10.x86_64 redhat-rpm-config-293-1.el10.noarch rpm-4.19.1.1-20.el10.x86_64 rpm-build-4.19.1.1-20.el10.x86_64 rpm-build-libs-4.19.1.1-20.el10.x86_64 rpm-libs-4.19.1.1-20.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10_1.x86_64 rust-toolset-srpm-macros-1.88.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-8.el10.x86_64 sqlite-libs-3.46.1-5.el10_1.x86_64 systemd-libs-257-13.el10.x86_64 tar-1.35-7.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10_0.x86_64 xz-5.6.2-4.el10_0.x86_64 xz-libs-5.6.2-4.el10_0.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-2.el10.x86_64 zstd-1.5.5-9.el10.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-rpkye_qg/pymol/pymol.spec) Config(child) 0 minutes 29 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/pymol-3.1.0-13.1.el10.src.rpm) Config(rhel+epel-10-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-10-x86_64-bootstrap-1766135395.026526/root. INFO: reusing tmpfs at /var/lib/mock/rhel+epel-10-x86_64-bootstrap-1766135395.026526/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-20.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10_1.x86_64 python3-dnf-4.20.0-18.el10.noarch python3-dnf-plugins-core-4.7.0-9.el10.noarch yum-4.20.0-18.el10.noarch Finish: chroot init Start: build phase for pymol-3.1.0-13.1.el10.src.rpm Start: build setup for pymol-3.1.0-13.1.el10.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 30 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 139 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - AppStr 32 kB/s | 4.1 kB 00:00 Red Hat CodeReady Linux Builder for RHEL 10 x86 148 kB/s | 4.0 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 112 kB/s | 31 kB 00:00 Dependencies resolved. ================================================================================================= Package Arch Version Repo Size ================================================================================================= Installing: catch2-devel x86_64 2.13.10-5.el10_0 epel 197 k desktop-file-utils x86_64 0.26-14.el10 appstream 75 k fdupes x86_64 1:2.4.0-1.el10_1 epel 59 k freeglut-devel x86_64 3.4.0-9.el10 appstream 968 k freetype-devel x86_64 2.13.2-8.el10 appstream 970 k gcc x86_64 14.3.1-2.1.el10 appstream 38 M gcc-c++ x86_64 14.3.1-2.1.el10 appstream 15 M glew-devel x86_64 2.2.0-9.el10_0 epel 217 k glm-devel noarch 1.0.1-5.el10 copr_base 248 k libappstream-glib x86_64 0.8.3-3.el10 appstream 414 k libpng-devel x86_64 2:1.6.40-8.el10 appstream 298 k libxml2-devel x86_64 2.12.5-9.el10_0 appstream 534 k mesa-libGL-devel x86_64 25.0.7-6.el10_1 appstream 30 k mmtf-cpp-devel x86_64 1.1.0-8.el10 copr_base 30 k msgpack-devel x86_64 3.1.0-17.el10_0 epel 312 k netcdf-devel x86_64 4.9.2-7.el10_0 epel 91 k pyproject-rpm-macros noarch 1.16.2-1.el10 crb 48 k python3-devel x86_64 3.12.11-3.el10 appstream 329 k python3-pillow x86_64 11.0.0-1.el10_0 epel 942 k python3-pyside6-devel x86_64 6.9.1-1.el10_1 epel 394 k python3-pytest noarch 7.4.3-5.el10 crb 760 k python3-qt5-devel x86_64 5.15.11-7.el10_1 epel 392 k Installing dependencies: abseil-cpp x86_64 20240722.1-1.el10_0 epel 590 k alsa-lib x86_64 1.2.14-1.el10 appstream 529 k annobin-docs noarch 12.99-1.el10 appstream 88 k annobin-plugin-gcc x86_64 12.99-1.el10 appstream 996 k aribb24 x86_64 1.0.3^20160216git5e9be27-1.el10_0 epel 40 k avahi-libs x86_64 0.9~rc2-2.el10 baseos 68 k blosc x86_64 1.21.6-4.el10_0 epel 58 k bluez-libs x86_64 5.83-2.el10 baseos 80 k brotli x86_64 1.1.0-6.el10 appstream 22 k brotli-devel x86_64 1.1.0-6.el10 appstream 39 k bzip2-devel x86_64 1.0.8-25.el10 appstream 217 k cairo x86_64 1.18.2-2.el10 appstream 717 k cairo-devel x86_64 1.18.2-2.el10 appstream 200 k cairo-gobject x86_64 1.18.2-2.el10 appstream 19 k chrpath x86_64 0.16-25.el10 baseos 34 k cjson x86_64 1.7.18-1.el10_0 epel 32 k clang-libs x86_64 20.1.8-1.el10 appstream 28 M clang-resource-filesystem x86_64 20.1.8-1.el10 appstream 17 k cmake x86_64 3.30.5-3.el10_0 appstream 12 M cmake-data noarch 3.30.5-3.el10_0 appstream 2.5 M cmake-filesystem x86_64 3.30.5-3.el10_0 appstream 24 k cmake-rpm-macros noarch 3.30.5-3.el10_0 appstream 16 k codec2 x86_64 1.2.0-5.el10_0~bootstrap epel 637 k cpp x86_64 14.3.1-2.1.el10 appstream 13 M cpuinfo x86_64 24.09.26-1.git1e83a2f.el10_1.1 epel 42 k cups-filesystem noarch 1:2.4.10-12.el10_1 baseos 11 k cups-libs x86_64 1:2.4.10-12.el10_1 baseos 261 k dbus x86_64 1:1.14.10-5.el10 baseos 8.5 k dbus-broker x86_64 36-4.el10 baseos 174 k dbus-common noarch 1:1.14.10-5.el10 baseos 19 k dbus-libs x86_64 1:1.14.10-5.el10 baseos 157 k default-fonts-core-sans noarch 4.1-3.el10 baseos 34 k double-conversion x86_64 3.4.0-1.el10_1 epel 51 k duktape x86_64 2.7.0-10.el10 baseos 173 k emacs-filesystem noarch 1:29.4-12.el10 appstream 10 k expat x86_64 2.7.1-1.el10_1.3 baseos 119 k fdk-aac-free x86_64 2.0.0-15.el10 appstream 341 k fftw-libs-single x86_64 3.3.10-15.el10 appstream 1.1 M flac-libs x86_64 1.4.3-6.el10 appstream 269 k fontconfig x86_64 2.15.0-7.el10 appstream 284 k fontconfig-devel x86_64 2.15.0-7.el10 appstream 179 k fonts-filesystem noarch 1:2.0.5-18.el10 baseos 9.9 k freeglut x86_64 3.4.0-9.el10 appstream 150 k freetype x86_64 2.13.2-8.el10 baseos 412 k fribidi x86_64 1.0.14-4.el10 appstream 97 k game-music-emu x86_64 0.6.3-16.el10_0 epel 153 k gcc-gfortran x86_64 14.3.1-2.1.el10 appstream 14 M gcc-plugin-annobin x86_64 14.3.1-2.1.el10 appstream 68 k gdk-pixbuf2 x86_64 2.42.12-4.el10_0 appstream 498 k gettext x86_64 0.22.5-6.el10 baseos 1.1 M gettext-envsubst x86_64 0.22.5-6.el10 baseos 40 k gettext-libs x86_64 0.22.5-6.el10 baseos 672 k gettext-runtime x86_64 0.22.5-6.el10 baseos 127 k giflib x86_64 5.2.1-22.el10 appstream 56 k glib2 x86_64 2.80.4-10.el10_1 baseos 3.0 M glib2-devel x86_64 2.80.4-10.el10_1 appstream 1.5 M glibc-devel x86_64 2.39-58.el10_1.2 appstream 602 k glx-utils x86_64 9.0.0-8.el10 appstream 75 k gnutls x86_64 3.8.10-2.el10 baseos 1.5 M google-noto-fonts-common noarch 20240401-5.el10 baseos 19 k google-noto-sans-vf-fonts noarch 20240401-5.el10 baseos 596 k graphene x86_64 1.10.6-10.el10 appstream 64 k graphite2 x86_64 1.3.14-17.el10 baseos 99 k graphite2-devel x86_64 1.3.14-17.el10 appstream 24 k groff-base x86_64 1.23.0-10.el10 baseos 1.1 M gsm x86_64 1.0.22-8.el10 appstream 40 k gstreamer1 x86_64 1.24.11-1.el10 appstream 1.6 M gstreamer1-plugins-bad-free-libs x86_64 1.24.11-2.el10_0 appstream 936 k gstreamer1-plugins-base x86_64 1.24.11-1.el10 appstream 2.2 M harfbuzz x86_64 8.4.0-6.el10 baseos 996 k harfbuzz-cairo x86_64 8.4.0-6.el10 appstream 29 k harfbuzz-devel x86_64 8.4.0-6.el10 appstream 457 k harfbuzz-icu x86_64 8.4.0-6.el10 appstream 16 k hdf-libs x86_64 4.3.0-1.el10_0 epel 292 k hdf5 x86_64 1.14.5-1.el10_0 epel 2.1 M hdf5-devel x86_64 1.14.5-1.el10_0 epel 1.4 M highway x86_64 1.2.0-7.el10_1 epel 470 k hwdata noarch 0.379-10.6.el10 baseos 1.7 M ilbc x86_64 3.0.4-12.el10_0 epel 54 k iso-codes noarch 4.16.0-6.el10 appstream 3.7 M jasper-libs x86_64 4.1.0-5.el10 appstream 165 k jbigkit-libs x86_64 2.1-31.el10 appstream 57 k json-glib x86_64 1.8.0-5.el10 baseos 172 k kernel-headers x86_64 6.12.0-124.21.1.el10_1 appstream 3.2 M keyutils-libs-devel x86_64 1.6.3-5.el10 appstream 65 k krb5-devel x86_64 1.21.3-8.el10_0 appstream 145 k lame-libs x86_64 3.100-19.el10 appstream 341 k lcms2 x86_64 2.16-6.el10 appstream 185 k libGLEW x86_64 2.2.0-9.el10_0 epel 176 k libICE x86_64 1.1.1-5.el10 appstream 78 k libSM x86_64 1.2.4-5.el10 appstream 46 k libX11 x86_64 1.8.10-1.el10 appstream 655 k libX11-common noarch 1.8.10-1.el10 appstream 203 k libX11-devel x86_64 1.8.10-1.el10 appstream 1.1 M libX11-xcb x86_64 1.8.10-1.el10 appstream 14 k libXau x86_64 1.0.11-8.el10 appstream 35 k libXau-devel x86_64 1.0.11-8.el10 appstream 17 k libXcomposite x86_64 0.4.6-5.el10 appstream 28 k libXdamage x86_64 1.1.6-5.el10 appstream 27 k libXext x86_64 1.3.6-3.el10 appstream 42 k libXext-devel x86_64 1.3.6-3.el10 appstream 91 k libXfixes x86_64 6.0.1-5.el10 appstream 22 k libXft x86_64 2.3.8-8.el10 appstream 76 k libXi x86_64 1.8.1-7.el10 appstream 43 k libXrandr x86_64 1.5.4-5.el10 appstream 31 k libXrender x86_64 0.9.11-8.el10 appstream 30 k libXrender-devel x86_64 0.9.11-8.el10 appstream 21 k libXtst x86_64 1.2.4-8.el10 appstream 23 k libXv x86_64 1.0.12-5.el10 appstream 21 k libXxf86vm x86_64 1.1.5-8.el10 appstream 21 k libaec x86_64 1.1.3-1.el10_0 epel 37 k libaec-devel x86_64 1.1.3-1.el10_0 epel 12 k libaom x86_64 3.13.1-1.el10_1 epel 1.8 M libaribcaption x86_64 1.1.1-1.el10_0 epel 110 k libasyncns x86_64 0.8-30.el10 appstream 33 k libavcodec-free x86_64 7.1.2-1.el10_1 epel 4.3 M libavformat-free x86_64 7.1.2-1.el10_1 epel 1.1 M libavutil-free x86_64 7.1.2-1.el10_1 epel 361 k libblkid-devel x86_64 2.40.2-13.el10 appstream 26 k libbluray x86_64 1.3.4-7.el10_0 epel 175 k libcom_err-devel x86_64 1.47.1-4.el10 appstream 17 k libcurl-devel x86_64 8.12.1-2.el10 appstream 948 k libdatrie x86_64 0.2.13-11.el10 appstream 35 k libdav1d x86_64 1.5.2-1.el10_1 epel 638 k libdrm x86_64 2.4.123-1.el10 appstream 167 k libdrm-devel x86_64 2.4.123-1.el10 appstream 185 k libdvdnav x86_64 6.1.1-10.el10 appstream 59 k libdvdread x86_64 6.1.3-9.el10 appstream 76 k libedit x86_64 3.1-52.20230828cvs.el10 baseos 108 k libevdev x86_64 1.13.1-6.el10 appstream 41 k libffi-devel x86_64 3.4.4-10.el10 appstream 29 k libgcrypt x86_64 1.11.0-5.el10 baseos 589 k libgfortran x86_64 14.3.1-2.1.el10 baseos 828 k libglvnd x86_64 1:1.7.0-7.el10 appstream 118 k libglvnd-core-devel x86_64 1:1.7.0-7.el10 appstream 20 k libglvnd-devel x86_64 1:1.7.0-7.el10 appstream 167 k libglvnd-egl x86_64 1:1.7.0-7.el10 appstream 39 k libglvnd-gles x86_64 1:1.7.0-7.el10 appstream 33 k libglvnd-glx x86_64 1:1.7.0-7.el10 appstream 134 k libglvnd-opengl x86_64 1:1.7.0-7.el10 appstream 40 k libgpg-error x86_64 1.50-2.el10 baseos 240 k libgudev x86_64 238-7.el10 baseos 38 k libicu x86_64 74.2-5.el10_0 baseos 10 M libicu-devel x86_64 74.2-5.el10_0 appstream 966 k libidn2-devel x86_64 2.3.7-3.el10 appstream 75 k libimagequant x86_64 4.0.3-5.el10_0 epel 312 k libinput x86_64 1.26.1-5.el10_0 appstream 225 k libjpeg-turbo x86_64 3.0.2-4.el10 appstream 255 k libjxl x86_64 1:0.10.4-1.el10_1 epel 1.2 M libkadm5 x86_64 1.21.3-8.el10_0 baseos 78 k liblc3 x86_64 1.0.4-7.el10 appstream 83 k libldac x86_64 2.0.2.3-17.el10 appstream 45 k libldb x86_64 4.22.4-106.el10_1 baseos 186 k liblerc x86_64 4.0.0-8.el10 appstream 221 k libmng x86_64 2.0.3-23.el10 appstream 191 k libmodplug x86_64 1:0.8.9.0-25.el10_0 epel 176 k libmount-devel x86_64 2.40.2-13.el10 appstream 26 k libmpc x86_64 1.3.1-7.el10 appstream 74 k libnghttp2-devel x86_64 1.64.0-2.el10 appstream 58 k libogg x86_64 2:1.3.5-10.el10 appstream 36 k libopenmpt x86_64 0.8.3-1.el10_1 epel 783 k libpciaccess x86_64 0.16-16.el10 baseos 30 k libpciaccess-devel x86_64 0.16-16.el10 appstream 14 k libpng x86_64 2:1.6.40-8.el10 baseos 122 k libpq x86_64 16.8-2.el10_0 baseos 257 k libproxy x86_64 0.5.5-4.el10 baseos 53 k libpsl-devel x86_64 0.21.5-6.el10 appstream 39 k libquadmath x86_64 14.3.1-2.1.el10 baseos 216 k libquadmath-devel x86_64 14.3.1-2.1.el10 appstream 56 k librabbitmq x86_64 0.14.0-3.el10 appstream 46 k libraqm x86_64 0.10.1-1.el10_0 epel 22 k librist x86_64 0.2.7-6.el10_0 epel 77 k librsvg2 x86_64 2.57.1-9.el10 appstream 1.5 M libsbc x86_64 2.0-6.el10 appstream 49 k libseccomp x86_64 2.5.6-1.el10 baseos 71 k libselinux-devel x86_64 3.9-1.el10 appstream 161 k libsepol-devel x86_64 3.9-1.el10 appstream 48 k libsmbclient x86_64 4.22.4-106.el10_1 baseos 75 k libsndfile x86_64 1.2.2-5.el10 appstream 218 k libsodium x86_64 1.0.20-2.el10_0 epel 177 k libssh-devel x86_64 0.11.1-5.el10_1 appstream 42 k libstdc++-devel x86_64 14.3.1-2.1.el10 appstream 2.8 M libswresample-free x86_64 7.1.2-1.el10_1 epel 68 k libtalloc x86_64 2.4.3-100.el10 baseos 34 k libtdb x86_64 1.4.13-100.el10 baseos 56 k libtevent x86_64 0.16.2-100.el10 baseos 51 k libthai x86_64 0.1.29-10.el10 appstream 217 k libtheora x86_64 1:1.1.1-39.el10 appstream 174 k libtiff x86_64 4.6.0-6.el10_1.1 appstream 213 k libtirpc x86_64 1.3.5-1.el10 baseos 98 k libtool-ltdl x86_64 2.4.7-13.el10 appstream 38 k libudfread x86_64 1.1.2-9.el10_0 epel 37 k libunwind x86_64 1.8.0-4.el10_0 epel 73 k libusb1 x86_64 1.0.28-1.el10 baseos 78 k libuv x86_64 1:1.51.0-1.el10_0 appstream 262 k libva x86_64 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2.4 M perl-locale noarch 1.12-512.2.el10_0 appstream 14 k perl-mro x86_64 1.29-512.2.el10_0 appstream 31 k perl-overload noarch 1.37-512.2.el10_0 appstream 46 k perl-overloading noarch 0.02-512.2.el10_0 appstream 14 k perl-parent noarch 1:0.241-512.el10 appstream 17 k perl-podlators noarch 1:5.01-511.el10 appstream 128 k perl-vars noarch 1.05-512.2.el10_0 appstream 14 k pipewire-libs x86_64 1.4.6-1.el10 appstream 2.5 M pixman x86_64 0.43.4-2.el10 appstream 288 k pixman-devel x86_64 0.43.4-2.el10 appstream 20 k publicsuffix-list noarch 20240107-5.el10 appstream 90 k pulseaudio-libs x86_64 17.0-6.el10 appstream 710 k pyside6-tools x86_64 6.9.1-1.el10_1 epel 60 k python-qt5-rpm-macros noarch 5.15.11-7.el10_1 epel 9.1 k python-rpm-macros noarch 3.12-10.el10 appstream 17 k python3 x86_64 3.12.11-3.el10 baseos 28 k python3-dbus x86_64 1.3.2-8.el10 baseos 162 k python3-iniconfig noarch 1.1.1-18.el10 crb 23 k python3-libs x86_64 3.12.11-3.el10 baseos 9.4 M python3-olefile noarch 0.47-5.el10_0 epel 73 k python3-packaging noarch 24.2-2.el10 baseos 157 k python3-pip-wheel noarch 23.3.2-7.el10 baseos 1.5 M python3-pluggy noarch 1.3.0-5.el10 crb 58 k python3-pyqt5-sip x86_64 12.15.0-3.el10_1 epel 72 k python3-pyside6 x86_64 6.9.1-1.el10_1 epel 10 M python3-qt5 x86_64 5.15.11-7.el10_1 epel 1.1 M python3-qt5-base x86_64 5.15.11-7.el10_1 epel 3.0 M python3-rpm-generators noarch 14-12.el10 appstream 32 k python3-rpm-macros noarch 3.12-10.el10 appstream 12 k python3-shiboken6 x86_64 6.9.1-1.el10_1 epel 294 k python3-shiboken6-devel x86_64 6.9.1-1.el10_1 epel 1.1 M qt5-filesystem x86_64 5.15.17-1.el10_1 epel 9.9 k qt5-qtbase x86_64 5.15.17-1.el10_1 epel 3.5 M qt5-qtbase-common noarch 5.15.17-1.el10_1 epel 11 k qt5-qtbase-devel x86_64 5.15.17-1.el10_1 epel 3.2 M qt5-qtbase-gui x86_64 5.15.17-1.el10_1 epel 6.4 M qt5-qtconnectivity x86_64 5.15.17-1.el10_1 epel 461 k qt5-qtdeclarative x86_64 5.15.17-1.el10_1 epel 4.2 M qt5-qtlocation x86_64 5.15.17-1.1.el10_1 epel 3.2 M qt5-qtmultimedia x86_64 5.15.17-1.el10_1 epel 795 k qt5-qtsensors x86_64 5.15.17-1.el10_1 epel 219 k qt5-qtserialport x86_64 5.15.17-1.el10_1 epel 65 k qt5-qtsvg x86_64 5.15.17-1.el10_1 epel 187 k qt5-qttools-common noarch 5.15.17-1.el10_1 epel 11 k qt5-qttools-libs-designer x86_64 5.15.17-1.el10_1 epel 2.7 M qt5-qttools-libs-help x86_64 5.15.17-1.el10_1 epel 156 k qt5-qtwebchannel x86_64 5.15.17-1.el10_1 epel 101 k qt5-qtwebsockets x86_64 5.15.17-1.el10_1 epel 86 k qt5-qtx11extras x86_64 5.15.17-1.el10_1 epel 34 k qt5-qtxmlpatterns x86_64 5.15.17-1.el10_1 epel 984 k qt5-rpm-macros noarch 5.15.17-1.el10_1 epel 10 k qt6-assistant x86_64 6.9.1-1.el10 appstream 606 k qt6-designer x86_64 6.9.1-1.el10 appstream 204 k qt6-filesystem x86_64 6.9.1-1.el10 appstream 14 k qt6-linguist x86_64 6.9.1-1.el10 appstream 982 k qt6-qt3d x86_64 6.9.1-1.el10 appstream 3.7 M qt6-qtbase x86_64 6.9.1-1.el10 appstream 4.2 M qt6-qtbase-common noarch 6.9.1-1.el10 appstream 12 k qt6-qtbase-devel x86_64 6.9.1-1.el10 appstream 4.2 M qt6-qtbase-gui x86_64 6.9.1-1.el10 appstream 7.9 M qt6-qtbase-mysql x86_64 6.9.1-1.el10 appstream 53 k qt6-qtbase-odbc x86_64 6.9.1-1.el10 appstream 65 k qt6-qtbase-postgresql x86_64 6.9.1-1.el10 appstream 60 k qt6-qtcharts x86_64 6.9.1-3.el10 appstream 859 k qt6-qtconnectivity x86_64 6.9.1-3.el10 appstream 519 k qt6-qtdatavis3d x86_64 6.9.1-2.el10 appstream 650 k qt6-qtdeclarative x86_64 6.9.1-2.el10 appstream 13 M qt6-qtdeclarative-devel x86_64 6.9.1-2.el10 appstream 4.6 M qt6-qtgraphs x86_64 6.9.1-1.el10_1 epel 893 k qt6-qthttpserver x86_64 6.9.1-1.el10_1 epel 107 k qt6-qtimageformats x86_64 6.9.1-2.el10 appstream 127 k qt6-qtlocation x86_64 6.9.1-1.el10 appstream 734 k qt6-qtmultimedia x86_64 6.9.1-1.el10 appstream 1.0 M qt6-qtnetworkauth x86_64 6.9.1-1.el10 appstream 128 k qt6-qtpdf x86_64 6.9.1-1.el10_1 epel 8.1 M qt6-qtpositioning x86_64 6.9.1-2.el10 appstream 454 k qt6-qtquick3d x86_64 6.9.1-1.el10_1.1 appstream 5.2 M qt6-qtquicktimeline x86_64 6.9.1-2.el10 appstream 96 k qt6-qtremoteobjects x86_64 6.9.1-3.el10 appstream 514 k qt6-qtscxml x86_64 6.9.1-3.el10 appstream 580 k qt6-qtsensors x86_64 6.9.1-3.el10 appstream 232 k qt6-qtserialbus x86_64 6.9.1-2.el10 appstream 305 k qt6-qtserialport x86_64 6.9.1-3.el10 appstream 81 k qt6-qtshadertools x86_64 6.9.1-1.el10 appstream 2.0 M qt6-qtspeech x86_64 6.9.1-1.el10 appstream 119 k qt6-qtsvg x86_64 6.9.1-2.el10_1.2 appstream 296 k qt6-qttools x86_64 6.9.1-1.el10 appstream 227 k qt6-qttools-common noarch 6.9.1-1.el10 appstream 13 k qt6-qttools-libs-designer x86_64 6.9.1-1.el10 appstream 3.0 M qt6-qttools-libs-designercomponents x86_64 6.9.1-1.el10 appstream 956 k qt6-qttools-libs-help x86_64 6.9.1-1.el10 appstream 210 k qt6-qtwebchannel x86_64 6.9.1-3.el10 appstream 156 k qt6-qtwebengine x86_64 6.9.1-1.el10_1 epel 87 M qt6-qtwebsockets x86_64 6.9.1-2.el10 appstream 110 k qt6-qtwebview x86_64 6.9.1-1.el10_1 epel 100 k qt6-rpm-macros noarch 6.9.1-1.el10 appstream 14 k rav1e-libs x86_64 0.7.1-8.el10_1 epel 1.0 M re2 x86_64 2:20251105-1.el10_1 epel 221 k redhat-text-vf-fonts noarch 4.1.0-1.el10 baseos 357 k rsvg-pixbuf-loader x86_64 2.57.1-9.el10 appstream 18 k samba-client-libs x86_64 4.22.4-106.el10_1 baseos 5.3 M samba-common noarch 4.22.4-106.el10_1 baseos 176 k samba-common-libs x86_64 4.22.4-106.el10_1 baseos 104 k shared-mime-info x86_64 2.3-8.el10 baseos 599 k shiboken6 x86_64 6.9.1-1.el10_1 epel 42 k snappy x86_64 1.1.10-7.el10 baseos 41 k soxr x86_64 0.1.3-17.el10_0 epel 83 k speex x86_64 1.2.0-19.el10 appstream 72 k spirv-tools-libs x86_64 2025.2-1.el10 appstream 1.5 M srt-libs x86_64 1.5.4-0.rc0.el10_0.1 epel 390 k svt-av1-libs x86_64 2.3.0-1.el10_0 epel 2.0 M sysprof-capture-devel x86_64 47.2-1.el10 appstream 60 k systemd x86_64 257-13.el10 baseos 5.7 M systemd-pam x86_64 257-13.el10 baseos 306 k systemd-rpm-macros noarch 257-13.el10 baseos 27 k twolame-libs x86_64 0.4.0-6.el10 appstream 72 k tzdata noarch 2025c-1.el10 baseos 904 k unixODBC x86_64 2.3.12-6.el10 appstream 500 k vim-filesystem noarch 2:9.1.083-6.el10_1 baseos 16 k vo-amrwbenc x86_64 0.1.3-21.el10_0 epel 80 k vulkan-headers noarch 1.4.313.0-1.el10 appstream 1.4 M vulkan-loader x86_64 1.4.313.0-1.el10 appstream 154 k vulkan-loader-devel x86_64 1.4.313.0-1.el10 appstream 13 k webrtc-audio-processing x86_64 1.3-5.el10 appstream 530 k xcb-util x86_64 0.4.1-7.el10 appstream 21 k xcb-util-cursor x86_64 0.1.4-6.el10 appstream 22 k xcb-util-image x86_64 0.4.1-7.el10 appstream 22 k xcb-util-keysyms x86_64 0.4.1-7.el10 appstream 17 k xcb-util-renderutil x86_64 0.3.10-7.el10 appstream 20 k xcb-util-wm x86_64 0.4.2-7.el10 appstream 35 k xkeyboard-config noarch 2.41-3.el10 appstream 1.0 M xml-common noarch 0.6.3-65.el10 appstream 36 k xorg-x11-proto-devel noarch 2024.1-3.el10 appstream 315 k xvidcore x86_64 1.3.7-12.el10_0 epel 269 k xz-devel x86_64 1:5.6.2-4.el10_0 appstream 64 k zeromq x86_64 4.3.5-18.el10_0 epel 451 k zlib-ng-compat-devel x86_64 2.2.3-2.el10 appstream 39 k zvbi x86_64 0.2.42-1.el10_0 epel 427 k Transaction Summary ================================================================================================= Install 474 Packages Total download size: 528 M Installed size: 1.8 G Downloading Packages: (1/474): chrpath-0.16-25.el10.x86_64.rpm 899 kB/s | 34 kB 00:00 (2/474): dbus-1.14.10-5.el10.x86_64.rpm 769 kB/s | 8.5 kB 00:00 (3/474): dbus-common-1.14.10-5.el10.noarch.rpm 1.8 MB/s | 19 kB 00:00 (4/474): dbus-libs-1.14.10-5.el10.x86_64.rpm 4.9 MB/s | 157 kB 00:00 (5/474): default-fonts-core-sans-4.1-3.el10.noa 3.4 MB/s | 34 kB 00:00 (6/474): duktape-2.7.0-10.el10.x86_64.rpm 15 MB/s | 173 kB 00:00 (7/474): fonts-filesystem-2.0.5-18.el10.noarch. 826 kB/s | 9.9 kB 00:00 (8/474): freetype-2.13.2-8.el10.x86_64.rpm 7.2 MB/s | 412 kB 00:00 (9/474): mmtf-cpp-devel-1.1.0-8.el10.x86_64.rpm 161 kB/s | 30 kB 00:00 (10/474): gettext-0.22.5-6.el10.x86_64.rpm 62 MB/s | 1.1 MB 00:00 (11/474): gettext-envsubst-0.22.5-6.el10.x86_64 2.3 MB/s | 40 kB 00:00 (12/474): gettext-libs-0.22.5-6.el10.x86_64.rpm 51 MB/s | 672 kB 00:00 (13/474): gettext-runtime-0.22.5-6.el10.x86_64. 7.6 MB/s | 127 kB 00:00 (14/474): google-noto-fonts-common-20240401-5.e 558 kB/s | 19 kB 00:00 (15/474): graphite2-1.3.14-17.el10.x86_64.rpm 9.8 MB/s | 99 kB 00:00 (16/474): google-noto-sans-vf-fonts-20240401-5. 13 MB/s | 596 kB 00:00 (17/474): groff-base-1.23.0-10.el10.x86_64.rpm 83 MB/s | 1.1 MB 00:00 (18/474): harfbuzz-8.4.0-6.el10.x86_64.rpm 66 MB/s | 996 kB 00:00 (19/474): json-glib-1.8.0-5.el10.x86_64.rpm 15 MB/s | 172 kB 00:00 (20/474): libedit-3.1-52.20230828cvs.el10.x86_6 11 MB/s | 108 kB 00:00 (21/474): libgcrypt-1.11.0-5.el10.x86_64.rpm 39 MB/s | 589 kB 00:00 (22/474): libgpg-error-1.50-2.el10.x86_64.rpm 9.4 MB/s | 240 kB 00:00 (23/474): libpciaccess-0.16-16.el10.x86_64.rpm 2.9 MB/s | 30 kB 00:00 (24/474): libgudev-238-7.el10.x86_64.rpm 1.1 MB/s | 38 kB 00:00 (25/474): libpng-1.6.40-8.el10.x86_64.rpm 12 MB/s | 122 kB 00:00 (26/474): libproxy-0.5.5-4.el10.x86_64.rpm 4.7 MB/s | 53 kB 00:00 (27/474): libtirpc-1.3.5-1.el10.x86_64.rpm 8.7 MB/s | 98 kB 00:00 (28/474): libpq-16.8-2.el10_0.x86_64.rpm 7.0 MB/s | 257 kB 00:00 (29/474): lmdb-libs-0.9.32-4.el10.x86_64.rpm 3.0 MB/s | 64 kB 00:00 (30/474): make-4.4.1-9.el10.x86_64.rpm 26 MB/s | 591 kB 00:00 (31/474): mariadb-connector-c-3.4.4-1.el10.x86_ 18 MB/s | 215 kB 00:00 (32/474): mariadb-connector-c-config-3.4.4-1.el 442 kB/s | 11 kB 00:00 (33/474): mpdecimal-2.5.1-12.el10.x86_64.rpm 2.7 MB/s | 92 kB 00:00 (34/474): ncurses-6.4-14.20240127.el10.x86_64.r 32 MB/s | 427 kB 00:00 (35/474): nettle-3.10.1-1.el10.x86_64.rpm 43 MB/s | 563 kB 00:00 (36/474): ocl-icd-2.3.2-8.el10.x86_64.rpm 2.2 MB/s | 69 kB 00:00 (37/474): python3-dbus-1.3.2-8.el10.x86_64.rpm 4.9 MB/s | 162 kB 00:00 (38/474): python3-packaging-24.2-2.el10.noarch. 9.3 MB/s | 157 kB 00:00 (39/474): python3-pip-wheel-23.3.2-7.el10.noarc 75 MB/s | 1.5 MB 00:00 (40/474): shared-mime-info-2.3-8.el10.x86_64.rp 23 MB/s | 599 kB 00:00 (41/474): snappy-1.1.10-7.el10.x86_64.rpm 3.6 MB/s | 41 kB 00:00 (42/474): libkadm5-1.21.3-8.el10_0.x86_64.rpm 7.7 MB/s | 78 kB 00:00 (43/474): avahi-libs-0.9~rc2-2.el10.x86_64.rpm 6.5 MB/s | 68 kB 00:00 (44/474): libicu-74.2-5.el10_0.x86_64.rpm 278 MB/s | 10 MB 00:00 (45/474): glm-devel-1.0.1-5.el10.noarch.rpm 461 kB/s | 248 kB 00:00 (46/474): bluez-libs-5.83-2.el10.x86_64.rpm 4.7 MB/s | 80 kB 00:00 (47/474): hwdata-0.379-10.6.el10.noarch.rpm 113 MB/s | 1.7 MB 00:00 (48/474): libgfortran-14.3.1-2.1.el10.x86_64.rp 64 MB/s | 828 kB 00:00 (49/474): dbus-broker-36-4.el10.x86_64.rpm 5.5 MB/s | 174 kB 00:00 (50/474): libquadmath-14.3.1-2.1.el10.x86_64.rp 15 MB/s | 216 kB 00:00 (51/474): libldb-4.22.4-106.el10_1.x86_64.rpm 9.5 MB/s | 186 kB 00:00 (52/474): gnutls-3.8.10-2.el10.x86_64.rpm 30 MB/s | 1.5 MB 00:00 (53/474): libseccomp-2.5.6-1.el10.x86_64.rpm 6.9 MB/s | 71 kB 00:00 (54/474): libtalloc-2.4.3-100.el10.x86_64.rpm 2.8 MB/s | 34 kB 00:00 (55/474): libtdb-1.4.13-100.el10.x86_64.rpm 4.3 MB/s | 56 kB 00:00 (56/474): libsmbclient-4.22.4-106.el10_1.x86_64 3.2 MB/s | 75 kB 00:00 (57/474): libtevent-0.16.2-100.el10.x86_64.rpm 3.6 MB/s | 51 kB 00:00 (58/474): libwbclient-4.22.4-106.el10_1.x86_64. 2.8 MB/s | 44 kB 00:00 (59/474): python3-3.12.11-3.el10.x86_64.rpm 2.6 MB/s | 28 kB 00:00 (60/474): libusb1-1.0.28-1.el10.x86_64.rpm 2.7 MB/s | 78 kB 00:00 (61/474): samba-client-libs-4.22.4-106.el10_1.x 152 MB/s | 5.3 MB 00:00 (62/474): redhat-text-vf-fonts-4.1.0-1.el10.noa 8.0 MB/s | 357 kB 00:00 (63/474): python3-libs-3.12.11-3.el10.x86_64.rp 163 MB/s | 9.4 MB 00:00 (64/474): samba-common-4.22.4-106.el10_1.noarch 12 MB/s | 176 kB 00:00 (65/474): samba-common-libs-4.22.4-106.el10_1.x 8.3 MB/s | 104 kB 00:00 (66/474): systemd-pam-257-13.el10.x86_64.rpm 29 MB/s | 306 kB 00:00 (67/474): systemd-257-13.el10.x86_64.rpm 226 MB/s | 5.7 MB 00:00 (68/474): cups-filesystem-2.4.10-12.el10_1.noar 795 kB/s | 11 kB 00:00 (69/474): systemd-rpm-macros-257-13.el10.noarch 997 kB/s | 27 kB 00:00 (70/474): cups-libs-2.4.10-12.el10_1.x86_64.rpm 24 MB/s | 261 kB 00:00 (71/474): glib2-2.80.4-10.el10_1.x86_64.rpm 157 MB/s | 3.0 MB 00:00 (72/474): vim-filesystem-9.1.083-6.el10_1.noarc 834 kB/s | 16 kB 00:00 (73/474): expat-2.7.1-1.el10_1.3.x86_64.rpm 11 MB/s | 119 kB 00:00 (74/474): tzdata-2025c-1.el10.noarch.rpm 75 MB/s | 904 kB 00:00 (75/474): brotli-1.1.0-6.el10.x86_64.rpm 1.2 MB/s | 22 kB 00:00 (76/474): cairo-gobject-1.18.2-2.el10.x86_64.rp 1.7 MB/s | 19 kB 00:00 (77/474): cairo-1.18.2-2.el10.x86_64.rpm 29 MB/s | 717 kB 00:00 (78/474): gsm-1.0.22-8.el10.x86_64.rpm 2.8 MB/s | 40 kB 00:00 (79/474): libXau-1.0.11-8.el10.x86_64.rpm 3.1 MB/s | 35 kB 00:00 (80/474): graphite2-devel-1.3.14-17.el10.x86_64 859 kB/s | 24 kB 00:00 (81/474): libXi-1.8.1-7.el10.x86_64.rpm 4.4 MB/s | 43 kB 00:00 (82/474): libXrender-devel-0.9.11-8.el10.x86_64 1.3 MB/s | 21 kB 00:00 (83/474): libXv-1.0.12-5.el10.x86_64.rpm 2.0 MB/s | 21 kB 00:00 (84/474): libdvdnav-6.1.1-10.el10.x86_64.rpm 5.0 MB/s | 59 kB 00:00 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perl-Term-ANSIColor-5.01-512.el10.noa 3.7 MB/s | 51 kB 00:00 (100/474): perl-Pod-Simple-3.45-511.el10.noarch 7.6 MB/s | 223 kB 00:00 (101/474): perl-constant-1.33-512.el10.noarch.r 1.3 MB/s | 25 kB 00:00 (102/474): perl-Term-Cap-1.18-511.el10.noarch.r 712 kB/s | 25 kB 00:00 (103/474): pulseaudio-libs-17.0-6.el10.x86_64.r 24 MB/s | 710 kB 00:00 (104/474): rsvg-pixbuf-loader-2.57.1-9.el10.x86 549 kB/s | 18 kB 00:00 (105/474): bzip2-devel-1.0.8-25.el10.x86_64.rpm 16 MB/s | 217 kB 00:00 (106/474): brotli-devel-1.1.0-6.el10.x86_64.rpm 1.4 MB/s | 39 kB 00:00 (107/474): xcb-util-keysyms-0.4.1-7.el10.x86_64 455 kB/s | 17 kB 00:00 (108/474): cairo-devel-1.18.2-2.el10.x86_64.rpm 7.2 MB/s | 200 kB 00:00 (109/474): fdk-aac-free-2.0.0-15.el10.x86_64.rp 9.9 MB/s | 341 kB 00:00 (110/474): freeglut-3.4.0-9.el10.x86_64.rpm 12 MB/s | 150 kB 00:00 (111/474): graphene-1.10.6-10.el10.x86_64.rpm 6.1 MB/s | 64 kB 00:00 (112/474): giflib-5.2.1-22.el10.x86_64.rpm 3.3 MB/s | 56 kB 00:00 (113/474): gstreamer1-1.24.11-1.el10.x86_64.rpm 97 MB/s | 1.6 MB 00:00 (114/474): harfbuzz-icu-8.4.0-6.el10.x86_64.rpm 1.2 MB/s | 16 kB 00:00 (115/474): jasper-libs-4.1.0-5.el10.x86_64.rpm 12 MB/s | 165 kB 00:00 (116/474): harfbuzz-cairo-8.4.0-6.el10.x86_64.r 688 kB/s | 29 kB 00:00 (117/474): fontconfig-2.15.0-7.el10.x86_64.rpm 3.0 MB/s | 284 kB 00:00 (118/474): lame-libs-3.100-19.el10.x86_64.rpm 23 MB/s | 341 kB 00:00 (119/474): libSM-1.2.4-5.el10.x86_64.rpm 3.9 MB/s | 46 kB 00:00 (120/474): libXcomposite-0.4.6-5.el10.x86_64.rp 872 kB/s | 28 kB 00:00 (121/474): libICE-1.1.1-5.el10.x86_64.rpm 1.2 MB/s | 78 kB 00:00 (122/474): libX11-1.8.10-1.el10.x86_64.rpm 12 MB/s | 655 kB 00:00 (123/474): libXext-1.3.6-3.el10.x86_64.rpm 2.0 MB/s | 42 kB 00:00 (124/474): libXtst-1.2.4-8.el10.x86_64.rpm 1.8 MB/s | 23 kB 00:00 (125/474): libdrm-devel-2.4.123-1.el10.x86_64.r 15 MB/s | 185 kB 00:00 (126/474): libXrandr-1.5.4-5.el10.x86_64.rpm 1.1 MB/s | 31 kB 00:00 (127/474): libdatrie-0.2.13-11.el10.x86_64.rpm 1.3 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orc-0.4.39-2.el10.x86_64.rpm 9.0 MB/s | 232 kB 00:00 (143/474): perl-Digest-1.20-511.el10.noarch.rpm 2.1 MB/s | 28 kB 00:00 (144/474): perl-File-Temp-0.231.100-512.el10.no 3.6 MB/s | 63 kB 00:00 (145/474): perl-Carp-1.54-511.el10.noarch.rpm 1.0 MB/s | 31 kB 00:00 (146/474): perl-Getopt-Long-2.58-3.el10.noarch. 2.7 MB/s | 68 kB 00:00 (147/474): perl-IO-Socket-IP-0.42-512.el10.noar 3.0 MB/s | 45 kB 00:00 (148/474): perl-MIME-Base64-3.16-511.el10.x86_6 2.6 MB/s | 34 kB 00:00 (149/474): perl-Socket-2.038-511.el10.x86_64.rp 5.3 MB/s | 59 kB 00:00 (150/474): perl-Pod-Usage-2.03-511.el10.noarch. 2.0 MB/s | 43 kB 00:00 (151/474): perl-Time-Local-1.350-511.el10.noarc 2.6 MB/s | 38 kB 00:00 (152/474): perl-Pod-Escapes-1.07-511.el10.noarc 608 kB/s | 22 kB 00:00 (153/474): speex-1.2.0-19.el10.x86_64.rpm 6.4 MB/s | 72 kB 00:00 (154/474): webrtc-audio-processing-1.3-5.el10.x 42 MB/s | 530 kB 00:00 (155/474): xcb-util-cursor-0.1.4-6.el10.x86_64. 1.4 MB/s | 22 kB 00:00 (156/474): 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Running transaction test Transaction test succeeded. 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Creating group 'kvm' with GID 36. Creating group 'render' with GID 105. Creating group 'sgx' with GID 106. Creating group 'systemd-journal' with GID 190. Creating group 'dbus' with GID 81. Creating user 'dbus' (System Message Bus) with UID 81 and GID 81. 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Installed: abseil-cpp-20240722.1-1.el10_0.x86_64 alsa-lib-1.2.14-1.el10.x86_64 annobin-docs-12.99-1.el10.noarch annobin-plugin-gcc-12.99-1.el10.x86_64 aribb24-1.0.3^20160216git5e9be27-1.el10_0.x86_64 avahi-libs-0.9~rc2-2.el10.x86_64 blosc-1.21.6-4.el10_0.x86_64 bluez-libs-5.83-2.el10.x86_64 brotli-1.1.0-6.el10.x86_64 brotli-devel-1.1.0-6.el10.x86_64 bzip2-devel-1.0.8-25.el10.x86_64 cairo-1.18.2-2.el10.x86_64 cairo-devel-1.18.2-2.el10.x86_64 cairo-gobject-1.18.2-2.el10.x86_64 catch2-devel-2.13.10-5.el10_0.x86_64 chrpath-0.16-25.el10.x86_64 cjson-1.7.18-1.el10_0.x86_64 clang-libs-20.1.8-1.el10.x86_64 clang-resource-filesystem-20.1.8-1.el10.x86_64 cmake-3.30.5-3.el10_0.x86_64 cmake-data-3.30.5-3.el10_0.noarch cmake-filesystem-3.30.5-3.el10_0.x86_64 cmake-rpm-macros-3.30.5-3.el10_0.noarch codec2-1.2.0-5.el10_0~bootstrap.x86_64 cpp-14.3.1-2.1.el10.x86_64 cpuinfo-24.09.26-1.git1e83a2f.el10_1.1.x86_64 cups-filesystem-1:2.4.10-12.el10_1.noarch cups-libs-1:2.4.10-12.el10_1.x86_64 dbus-1:1.14.10-5.el10.x86_64 dbus-broker-36-4.el10.x86_64 dbus-common-1:1.14.10-5.el10.noarch dbus-libs-1:1.14.10-5.el10.x86_64 default-fonts-core-sans-4.1-3.el10.noarch desktop-file-utils-0.26-14.el10.x86_64 double-conversion-3.4.0-1.el10_1.x86_64 duktape-2.7.0-10.el10.x86_64 emacs-filesystem-1:29.4-12.el10.noarch expat-2.7.1-1.el10_1.3.x86_64 fdk-aac-free-2.0.0-15.el10.x86_64 fdupes-1:2.4.0-1.el10_1.x86_64 fftw-libs-single-3.3.10-15.el10.x86_64 flac-libs-1.4.3-6.el10.x86_64 fontconfig-2.15.0-7.el10.x86_64 fontconfig-devel-2.15.0-7.el10.x86_64 fonts-filesystem-1:2.0.5-18.el10.noarch freeglut-3.4.0-9.el10.x86_64 freeglut-devel-3.4.0-9.el10.x86_64 freetype-2.13.2-8.el10.x86_64 freetype-devel-2.13.2-8.el10.x86_64 fribidi-1.0.14-4.el10.x86_64 game-music-emu-0.6.3-16.el10_0.x86_64 gcc-14.3.1-2.1.el10.x86_64 gcc-c++-14.3.1-2.1.el10.x86_64 gcc-gfortran-14.3.1-2.1.el10.x86_64 gcc-plugin-annobin-14.3.1-2.1.el10.x86_64 gdk-pixbuf2-2.42.12-4.el10_0.x86_64 gettext-0.22.5-6.el10.x86_64 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qt6-qtsvg-6.9.1-2.el10_1.2.x86_64 qt6-qttools-6.9.1-1.el10.x86_64 qt6-qttools-common-6.9.1-1.el10.noarch qt6-qttools-libs-designer-6.9.1-1.el10.x86_64 qt6-qttools-libs-designercomponents-6.9.1-1.el10.x86_64 qt6-qttools-libs-help-6.9.1-1.el10.x86_64 qt6-qtwebchannel-6.9.1-3.el10.x86_64 qt6-qtwebengine-6.9.1-1.el10_1.x86_64 qt6-qtwebsockets-6.9.1-2.el10.x86_64 qt6-qtwebview-6.9.1-1.el10_1.x86_64 qt6-rpm-macros-6.9.1-1.el10.noarch rav1e-libs-0.7.1-8.el10_1.x86_64 re2-2:20251105-1.el10_1.x86_64 redhat-text-vf-fonts-4.1.0-1.el10.noarch rsvg-pixbuf-loader-2.57.1-9.el10.x86_64 samba-client-libs-4.22.4-106.el10_1.x86_64 samba-common-4.22.4-106.el10_1.noarch samba-common-libs-4.22.4-106.el10_1.x86_64 shared-mime-info-2.3-8.el10.x86_64 shiboken6-6.9.1-1.el10_1.x86_64 snappy-1.1.10-7.el10.x86_64 soxr-0.1.3-17.el10_0.x86_64 speex-1.2.0-19.el10.x86_64 spirv-tools-libs-2025.2-1.el10.x86_64 srt-libs-1.5.4-0.rc0.el10_0.1.x86_64 svt-av1-libs-2.3.0-1.el10_0.x86_64 sysprof-capture-devel-47.2-1.el10.x86_64 systemd-257-13.el10.x86_64 systemd-pam-257-13.el10.x86_64 systemd-rpm-macros-257-13.el10.noarch twolame-libs-0.4.0-6.el10.x86_64 tzdata-2025c-1.el10.noarch unixODBC-2.3.12-6.el10.x86_64 vim-filesystem-2:9.1.083-6.el10_1.noarch vo-amrwbenc-0.1.3-21.el10_0.x86_64 vulkan-headers-1.4.313.0-1.el10.noarch vulkan-loader-1.4.313.0-1.el10.x86_64 vulkan-loader-devel-1.4.313.0-1.el10.x86_64 webrtc-audio-processing-1.3-5.el10.x86_64 xcb-util-0.4.1-7.el10.x86_64 xcb-util-cursor-0.1.4-6.el10.x86_64 xcb-util-image-0.4.1-7.el10.x86_64 xcb-util-keysyms-0.4.1-7.el10.x86_64 xcb-util-renderutil-0.3.10-7.el10.x86_64 xcb-util-wm-0.4.2-7.el10.x86_64 xkeyboard-config-2.41-3.el10.noarch xml-common-0.6.3-65.el10.noarch xorg-x11-proto-devel-2024.1-3.el10.noarch xvidcore-1.3.7-12.el10_0.x86_64 xz-devel-1:5.6.2-4.el10_0.x86_64 zeromq-4.3.5-18.el10_0.x86_64 zlib-ng-compat-devel-2.2.3-2.el10.x86_64 zvbi-0.2.42-1.el10_0.x86_64 Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 3.3 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 47 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - AppStr 84 kB/s | 4.1 kB 00:00 Red Hat CodeReady Linux Builder for RHEL 10 x86 90 kB/s | 4.0 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 111 kB/s | 31 kB 00:00 Package catch2-devel-2.13.10-5.el10_0.x86_64 is already installed. Package desktop-file-utils-0.26-14.el10.x86_64 is already installed. Package fdupes-1:2.4.0-1.el10_1.x86_64 is already installed. Package freeglut-devel-3.4.0-9.el10.x86_64 is already installed. Package freetype-devel-2.13.2-8.el10.x86_64 is already installed. Package gcc-14.3.1-2.1.el10.x86_64 is already installed. Package gcc-c++-14.3.1-2.1.el10.x86_64 is already installed. Package glew-devel-2.2.0-9.el10_0.x86_64 is already installed. Package glm-devel-1.0.1-5.el10.noarch is already installed. Package mesa-libGL-devel-25.0.7-6.el10_1.x86_64 is already installed. Package libappstream-glib-0.8.3-3.el10.x86_64 is already installed. Package libpng-devel-2:1.6.40-8.el10.x86_64 is already installed. Package libxml2-devel-2.12.5-9.el10_0.x86_64 is already installed. Package mmtf-cpp-devel-1.1.0-8.el10.x86_64 is already installed. Package msgpack-devel-3.1.0-17.el10_0.x86_64 is already installed. Package netcdf-devel-4.9.2-7.el10_0.x86_64 is already installed. Package pyproject-rpm-macros-1.16.2-1.el10.noarch is already installed. Package python3-devel-3.12.11-3.el10.x86_64 is already installed. Package python3-pillow-11.0.0-1.el10_0.x86_64 is already installed. Package python3-pyside6-devel-6.9.1-1.el10_1.x86_64 is already installed. Package python3-pytest-7.4.3-5.el10.noarch is already installed. Package python3-qt5-devel-5.15.11-7.el10_1.x86_64 is already installed. Dependencies resolved. Nothing to do. Complete! Finish: build setup for pymol-3.1.0-13.1.el10.src.rpm Start: rpmbuild pymol-3.1.0-13.1.el10.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ojLzLu + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pymol-open-source-3.1.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pymol-open-source-3.1.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pymol-open-source-3.1.0 + rm -rf /builddir/build/BUILD/pymol-open-source-3.1.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/pymol-open-source-3.1.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/pymol-wmclass-main.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/pymol-wmclass-pmgapp.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/pymol-mmtf.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/pymol-pyproject.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + ln -sr modules/web modules/pymol_web + sed -e 's|1.26.4,<2|1.26.4,<3|g' -i ./pyproject.toml + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.GA3qeL + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-3.1.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement not satisfied: numpy>=1.26.4,<3 Handling setuptools>=69.0.0 from build-system.requires Requirement not satisfied: setuptools>=69.0.0 Handling wheel>=0.41.0 from build-system.requires Requirement not satisfied: wheel>=0.41.0 Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 6.8 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 103 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - AppStr 153 kB/s | 4.1 kB 00:00 Red Hat CodeReady Linux Builder for RHEL 10 x86 157 kB/s | 4.0 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 112 kB/s | 31 kB 00:00 Package catch2-devel-2.13.10-5.el10_0.x86_64 is already installed. Package desktop-file-utils-0.26-14.el10.x86_64 is already installed. Package fdupes-1:2.4.0-1.el10_1.x86_64 is already installed. Package freeglut-devel-3.4.0-9.el10.x86_64 is already installed. Package freetype-devel-2.13.2-8.el10.x86_64 is already installed. Package gcc-14.3.1-2.1.el10.x86_64 is already installed. Package gcc-c++-14.3.1-2.1.el10.x86_64 is already installed. Package glew-devel-2.2.0-9.el10_0.x86_64 is already installed. Package glm-devel-1.0.1-5.el10.noarch is already installed. Package mesa-libGL-devel-25.0.7-6.el10_1.x86_64 is already installed. Package libappstream-glib-0.8.3-3.el10.x86_64 is already installed. Package libpng-devel-2:1.6.40-8.el10.x86_64 is already installed. Package libxml2-devel-2.12.5-9.el10_0.x86_64 is already installed. Package mmtf-cpp-devel-1.1.0-8.el10.x86_64 is already installed. Package msgpack-devel-3.1.0-17.el10_0.x86_64 is already installed. Package netcdf-devel-4.9.2-7.el10_0.x86_64 is already installed. Package pyproject-rpm-macros-1.16.2-1.el10.noarch is already installed. Package pyproject-rpm-macros-1.16.2-1.el10.noarch is already installed. Package python3-devel-3.12.11-3.el10.x86_64 is already installed. Package python3-devel-3.12.11-3.el10.x86_64 is already installed. Package python3-pillow-11.0.0-1.el10_0.x86_64 is already installed. Package python3-pyside6-devel-6.9.1-1.el10_1.x86_64 is already installed. Package python3-pytest-7.4.3-5.el10.noarch is already installed. Package python3-qt5-devel-5.15.11-7.el10_1.x86_64 is already installed. Package python3-packaging-24.2-2.el10.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-numpy x86_64 1:1.26.4-5.el10 appstream 6.7 M python3-pip noarch 23.3.2-7.el10 appstream 3.2 M python3-setuptools noarch 69.0.3-12.el10_0 baseos 1.6 M python3-wheel noarch 1:0.41.2-5.el10 crb 171 k Installing dependencies: flexiblas x86_64 3.4.2-3.el10 appstream 27 k flexiblas-netlib x86_64 3.4.2-3.el10 appstream 3.2 M flexiblas-openblas-openmp x86_64 3.4.2-3.el10 appstream 19 k openblas x86_64 0.3.29-2.el10 appstream 44 k openblas-openmp x86_64 0.3.29-2.el10 appstream 5.3 M Transaction Summary ================================================================================ Install 9 Packages Total download size: 20 M Installed size: 113 M Downloading Packages: (1/9): flexiblas-3.4.2-3.el10.x86_64.rpm 531 kB/s | 27 kB 00:00 (2/9): flexiblas-openblas-openmp-3.4.2-3.el10.x 1.5 MB/s | 19 kB 00:00 (3/9): python3-setuptools-69.0.3-12.el10_0.noar 24 MB/s | 1.6 MB 00:00 (4/9): flexiblas-netlib-3.4.2-3.el10.x86_64.rpm 43 MB/s | 3.2 MB 00:00 (5/9): python3-pip-23.3.2-7.el10.noarch.rpm 140 MB/s | 3.2 MB 00:00 (6/9): openblas-0.3.29-2.el10.x86_64.rpm 2.9 MB/s | 44 kB 00:00 (7/9): python3-wheel-0.41.2-5.el10.noarch.rpm 15 MB/s | 171 kB 00:00 (8/9): python3-numpy-1.26.4-5.el10.x86_64.rpm 108 MB/s | 6.7 MB 00:00 (9/9): openblas-openmp-0.3.29-2.el10.x86_64.rpm 126 MB/s | 5.3 MB 00:00 -------------------------------------------------------------------------------- Total 152 MB/s | 20 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : openblas-0.3.29-2.el10.x86_64 1/9 Installing : openblas-openmp-0.3.29-2.el10.x86_64 2/9 Installing : flexiblas-netlib-3.4.2-3.el10.x86_64 3/9 Installing : flexiblas-openblas-openmp-3.4.2-3.el10.x86_64 4/9 Installing : flexiblas-3.4.2-3.el10.x86_64 5/9 Installing : python3-numpy-1:1.26.4-5.el10.x86_64 6/9 Installing : python3-wheel-1:0.41.2-5.el10.noarch 7/9 Installing : python3-pip-23.3.2-7.el10.noarch 8/9 Installing : python3-setuptools-69.0.3-12.el10_0.noarch 9/9 Running scriptlet: python3-setuptools-69.0.3-12.el10_0.noarch 9/9 Installed products updated. Installed: flexiblas-3.4.2-3.el10.x86_64 flexiblas-netlib-3.4.2-3.el10.x86_64 flexiblas-openblas-openmp-3.4.2-3.el10.x86_64 openblas-0.3.29-2.el10.x86_64 openblas-openmp-0.3.29-2.el10.x86_64 python3-numpy-1:1.26.4-5.el10.x86_64 python3-pip-23.3.2-7.el10.noarch python3-setuptools-69.0.3-12.el10_0.noarch python3-wheel-1:0.41.2-5.el10.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.NhYbEM + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-3.1.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 1.26.4) Handling setuptools>=69.0.0 from build-system.requires Requirement satisfied: setuptools>=69.0.0 (installed: setuptools 69.0.3) Handling wheel>=0.41.0 from build-system.requires Requirement satisfied: wheel>=0.41.0 (installed: wheel 0.41.2) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 1.26.4) Handling pillow==10.3.0 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pillow==10.3.0 Handling pytest==8.2.2 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pytest==8.2.2 + cat /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 1.3 kB/s | 1.5 kB 00:01 Red Hat Enterprise Linux 10 for x86_64 - BaseOS 47 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux 10 for x86_64 - AppStr 45 kB/s | 4.1 kB 00:00 Red Hat CodeReady Linux Builder for RHEL 10 x86 42 kB/s | 4.0 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 115 kB/s | 31 kB 00:00 Package python3-numpy-1:1.26.4-5.el10.x86_64 is already installed. Package catch2-devel-2.13.10-5.el10_0.x86_64 is already installed. Package desktop-file-utils-0.26-14.el10.x86_64 is already installed. Package fdupes-1:2.4.0-1.el10_1.x86_64 is already installed. Package freeglut-devel-3.4.0-9.el10.x86_64 is already installed. Package freetype-devel-2.13.2-8.el10.x86_64 is already installed. Package gcc-14.3.1-2.1.el10.x86_64 is already installed. Package gcc-c++-14.3.1-2.1.el10.x86_64 is already installed. Package glew-devel-2.2.0-9.el10_0.x86_64 is already installed. Package glm-devel-1.0.1-5.el10.noarch is already installed. Package mesa-libGL-devel-25.0.7-6.el10_1.x86_64 is already installed. Package libappstream-glib-0.8.3-3.el10.x86_64 is already installed. Package libpng-devel-2:1.6.40-8.el10.x86_64 is already installed. Package libxml2-devel-2.12.5-9.el10_0.x86_64 is already installed. Package mmtf-cpp-devel-1.1.0-8.el10.x86_64 is already installed. Package msgpack-devel-3.1.0-17.el10_0.x86_64 is already installed. Package netcdf-devel-4.9.2-7.el10_0.x86_64 is already installed. Package pyproject-rpm-macros-1.16.2-1.el10.noarch is already installed. Package pyproject-rpm-macros-1.16.2-1.el10.noarch is already installed. Package python3-devel-3.12.11-3.el10.x86_64 is already installed. Package python3-devel-3.12.11-3.el10.x86_64 is already installed. Package python3-pillow-11.0.0-1.el10_0.x86_64 is already installed. Package python3-pyside6-devel-6.9.1-1.el10_1.x86_64 is already installed. Package python3-pytest-7.4.3-5.el10.noarch is already installed. Package python3-qt5-devel-5.15.11-7.el10_1.x86_64 is already installed. Package python3-packaging-24.2-2.el10.noarch is already installed. Package python3-pip-23.3.2-7.el10.noarch is already installed. Package python3-setuptools-69.0.3-12.el10_0.noarch is already installed. Package python3-wheel-1:0.41.2-5.el10.noarch is already installed. Dependencies resolved. Nothing to do. Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1766102400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.VQnrjY + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-3.1.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 1.26.4) Handling setuptools>=69.0.0 from build-system.requires Requirement satisfied: setuptools>=69.0.0 (installed: setuptools 69.0.3) Handling wheel>=0.41.0 from build-system.requires Requirement satisfied: wheel>=0.41.0 (installed: wheel 0.41.2) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 1.26.4) Handling pillow==10.3.0 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pillow==10.3.0 Handling pytest==8.2.2 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pytest==8.2.2 + cat /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.giLtyC + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 + mkdir -p /builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py -C=use-openmp=yes -C=testing=true -C=use-msgpackc=c++11 /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir Processing /builddir/build/BUILD/pymol-open-source-3.1.0 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running build_ext cmake /builddir/build/BUILD/pymol-open-source-3.1.0 -DTARGET_NAME=_cmd -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/pymol -DCMAKE_BUILD_TYPE=Release -DALL_INC_DIR=include;contrib/uiuc/plugins/include;ov/src;layer0;layer1;layer2;layer3;layer4;layer5;build/generated;contrib/uiuc/plugins/molfile_plugin/src;contrib/mmtf-c;layerCTest;/usr/lib64/python3.12/site-packages/numpy/core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.12;/usr/include/python3.12; 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o -MF CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o.d -o CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/build/generated/ShaderText.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerInitAll’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 271 | if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 273 | if(ok) { | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerFreeAll’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 411 | if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 413 | return ok; | ^~~~~~ [ 1%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘DEN_read_volumetric_data’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 970 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 971 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘POT_read_volumetric_data’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1113 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1114 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘abinit_header’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1511 | fread(skip, 1, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘GEO_read_next_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 619 | fscanf(data->file, "%*s %f %f %f", &x, &y, &z); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 2%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] 1097 | static void whereami(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] 1077 | static void thisline(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] 1028 | static int fpexpftoc(char *ftocstr) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] 1006 | static int have_keyline(FILE *file, const char *keystring1, | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:962:12: warning: ‘goto_keyline’ defined but not used [-Wunused-function] 962 | static int goto_keyline(FILE *file, ...) { | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] 901 | static char *strtoupper(char *s) { | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] 895 | static int iswhiteline(char *s) { | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:846:13: warning: ‘eatwhitelines’ defined but not used [-Wunused-function] 846 | static void eatwhitelines(FILE *file) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:13: warning: ‘eatline’ defined but not used [-Wunused-function] 835 | static void eatline(FILE * fd, int n) | ^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] 711 | static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] 585 | static void print_matrix4(const float mat[16]) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:540:13: warning: ‘angular_momentum_expon’ defined but not used [-Wunused-function] 540 | static void angular_momentum_expon(int *ang_mom_expon, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] 507 | static void del_wavefunction(qm_timestep_t *ts) { | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] 490 | static void replace_wavefunction(qm_timestep_t *ts, int n) { | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:471:27: warning: ‘add_wavefunction’ defined but not used [-Wunused-function] 471 | static qm_wavefunction_t* add_wavefunction(qm_timestep_t *ts) { | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:437:18: warning: ‘init_qmdata’ defined but not used [-Wunused-function] 437 | static qmdata_t* init_qmdata() { | ^~~~~~~~~~~ [ 2%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 243 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 252 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_bonds_aux(void*, int*, int**, int**, float**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 328 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 346 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fgets(nextline, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 419 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 203 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘void* open_bgf_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 3%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function ‘open_binpos_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 64 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘read_bgf_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:120:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 224 [-Wstringop-truncation] 120 | strncpy(numstr, record + 31, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:125:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 214 [-Wstringop-truncation] 125 | strncpy(numstr+10, record + 41, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:130:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 204 [-Wstringop-truncation] 130 | strncpy(numstr+20, record + 51, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:120:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 224 [-Wstringop-truncation] 120 | strncpy(numstr, record + 31, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:125:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 214 [-Wstringop-truncation] 125 | strncpy(numstr+10, record + 41, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:130:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 204 [-Wstringop-truncation] 130 | strncpy(numstr+20, record + 51, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘read_bgf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:144:10: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 242 [-Wstringop-truncation] 144 | strncpy(name, record + 13, 5); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:149:10: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 236 [-Wstringop-truncation] 149 | strncpy(resname, record + 19, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:167:10: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 194 [-Wstringop-truncation] 167 | strncpy(type, record+61, 5); | ^ [ 3%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp [ 4%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 326 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 339 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 344 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 349 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 363 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 373 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 266 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 272 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 295 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 305 | fgets(line, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘open_car_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 169 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 179 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 182 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 210 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 213 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 224 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 226 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 234 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 245 | fgets(line, LINESIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘int read_brix_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 247 | fread(brick, sizeof(char), 512, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘void* open_brix_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fscanf(fd, "%3s", keyWord); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | fscanf(fd, " %s %f %f %f %f %f %f", keyWord, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 123 | fscanf(fd, " %s %f", keyWord, &prod); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(fd, " %s %f", keyWord, &plus); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 135 | fscanf(fd, " %s %f", keyWord, &sigma); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:29: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] 127 | sprintf(atom->resname, "%d", resid); | ^~ In function ‘read_car_structure_line’, inlined from ‘read_car_structure’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:28: note: directive argument in the range [-2147483648, 9999999] 127 | sprintf(atom->resname, "%d", resid); | ^~~~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: In function ‘sprintf’, inlined from ‘read_car_structure_line’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:5, inlined from ‘read_car_structure’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 12 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp [ 4%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c [ 5%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘int read_ccp4_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:495:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 495 | if ( fread(rowdata, sizeof(char), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:525:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 525 | if ( fread(rowdata, sizeof(unsigned char), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:556:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 556 | if (fread(rowdata, sizeof(float), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:588:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 588 | if (fread(rowdata, sizeof(short), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:623:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 623 | if (fread(rowdata, sizeof(unsigned short), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:655:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 655 | if ( fread(rowdata, sizeof(uchar3), extent[0], fd) != extent[0] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 5%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘void* open_ccp4_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | fgets(symData, 81, fd); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:42: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 6%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘bool MMTF_unpack_from_file(const char*, MMTF_container*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:1079:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1079 | fread(buffer, fileLen, 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function ‘read_dcdstep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable ‘readlen’ set but not used [-Wunused-but-set-variable] 546 | fio_size_t readlen; /* number of bytes actually read */ | ^~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 609 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 605 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function ‘void* open_cube_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:175:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 175 | fgets(readbuf, 1023, cube->fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 181 | fgets(readbuf, 1023, cube->fd); // skip second header line | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 326 | fgets(readbuf, 1023, cube->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 337 | fgets(readbuf, 1023, cube->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 339 | fscanf(cube->fd, "%d", &cube->nsets); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 344 | fscanf(cube->fd, "%d", &orb); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 349 | fgets(readbuf, 1023, cube->fd); // gobble up rest of line | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:107:13: warning: ‘void cube_buildrotmat(cube_t*, float*, float*, float*)’ defined but not used [-Wunused-function] 107 | static void cube_buildrotmat(cube_t *cube, float *o, float *a, float *b) | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘open_ccp4_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:279:3: warning: ‘dataOffset’ may be used uninitialized [-Wmaybe-uninitialized] 279 | if (dataOffset != (CCP4HDSIZE + symBytes)) { | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:89:8: note: ‘dataOffset’ was declared here 89 | long dataOffset, filesize; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function ‘open_cube_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:179:10: warning: ‘__strncat_chk’ output may be truncated copying 240 bytes from a string of length 1023 [-Wstringop-truncation] 179 | strncat(voltmpl.dataname, readbuf, 240); // 240 is max space left after | ^ [ 6%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 292 | if (NULL == fgets(fbuffer, 1024, data->file)) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:295:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 295 | if (NULL == fgets(fbuffer, 1024, data->file)) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:669:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 669 | fgets(fbuffer, 1024, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:554:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 554 | fgets(fbuffer, 1024, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:362:5: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] 362 | strncpy(atom->name, buf, sizeof(atom->name)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:267:5: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] 267 | strncpy(atom->name, buf, sizeof(atom->name)); | ^ [ 7%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘int read_dsn6_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 233 | fread(brick, sizeof(char), 512, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘void* open_dsn6_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | fread(fileHeader, sizeof(short), 19, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] 110 | static void swap4_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In function ‘MMTF_parser_integer_decode_from_16(short const*, unsigned int, int, unsigned int*)’, inlined from ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:702:59, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:578:50: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 578 | float* output = (float*)MALLOC_ARRAY(float, (*output_length)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:699:18: note: ‘step1_length’ was declared here 699 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:740:72: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 740 | int32_t* output = MMTF_parser_recursive_indexing_decode_from_16(step1, step1_length, output_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:737:18: note: ‘step1_length’ was declared here 737 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:713:71: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 713 | int32_t* step2 = MMTF_parser_recursive_indexing_decode_from_16(step1, step1_length, &step2_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:709:18: note: ‘step1_length’ was declared here 709 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:685:71: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 685 | int32_t* step2 = MMTF_parser_recursive_indexing_decode_from_16(step1, step1_length, &step2_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:681:18: note: ‘step1_length’ was declared here 681 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:671:55: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 671 | int32_t* step2 = MMTF_parser_run_length_decode(step1, step1_length, &step2_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:667:18: note: ‘step1_length’ was declared here 667 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:657:55: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 657 | int32_t* step2 = MMTF_parser_run_length_decode(step1, step1_length, &step2_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:653:18: note: ‘step1_length’ was declared here 653 | uint32_t step1_length; | ^~~~~~~~~~~~ In function ‘MMTF_parser_decode_apply_strategy(char const*, unsigned int, unsigned int*, int, int, int*)’, inlined from ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:633:56: warning: ‘step1_length’ may be used uninitialized [-Wmaybe-uninitialized] 633 | int32_t* output = MMTF_parser_run_length_decode(step1, step1_length, output_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp: In function ‘MMTF_parser_fetch_typed_array(msgpack::v2::object const*, unsigned long*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:630:18: note: ‘step1_length’ was declared here 630 | uint32_t step1_length; | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:873:5: warning: ‘typecheck’ may be used uninitialized [-Wmaybe-uninitialized] 873 | if (typecode != typecheck) { | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:868:9: note: ‘typecheck’ was declared here 868 | int typecheck; | ^~~~~~~~~ [ 7%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp [ 8%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘int read_edm_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:240:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 240 | fgets(readbuf, 13, edm->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘void eatline(FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp [ 8%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘have_gamess’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1106:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] 1106 | char word[3][BUFSIZ]; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_stats’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2264:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] 2264 | char word[7][BUFSIZ]; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_wavefunction’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:3573:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] 3573 | char word[6][BUFSIZ]; | ^~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 840 | fgets(readbuf, 1024, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function ‘void* open_fs4_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fread(&dataBegin, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] 133 | static void strnwscpy(char *target, const char *source, const int len) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1002:13: warning: ‘print_input_data’ defined but not used [-Wunused-function] 1002 | static void print_input_data(qmdata_t *data) { | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] 109 | static float get_pte_vdw_radius(const int idx) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] 102 | static float get_pte_mass(const int idx) | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] 95 | static const char *get_pte_label(const int idx) | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] 1097 | static void whereami(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] 1077 | static void thisline(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] 1028 | static int fpexpftoc(char *ftocstr) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] 901 | static char *strtoupper(char *s) { | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] 895 | static int iswhiteline(char *s) { | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] 585 | static void print_matrix4(const float mat[16]) { | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] 110 | static void swap4_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vmddir.h:145:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function] 145 | static int vmd_file_is_executable(const char * filename) { | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘read_gamess_rundata’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:615:3: warning: ‘strncpy’ output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] 615 | strncpy(sys_data->basis_string, data->basis_string, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:620:3: warning: ‘strncpy’ output may be truncated copying 4096 bytes from a string of length 8191 [-Wstringop-truncation] 620 | strncpy(sys_data->runtitle, data->runtitle, sizeof(sys_data->runtitle)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:621:3: warning: ‘strncpy’ output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] 621 | strncpy(sys_data->geometry, data->geometry, sizeof(sys_data->geometry)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:622:3: warning: ‘strncpy’ output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] 622 | strncpy(sys_data->version_string, data->version_string, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_coordinates’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] 1618 | strncpy(atm->type, atname, sizeof(atm->type)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘void line3(FILE*, GRASSP*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 186 | fread(line3, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:3: note: in expansion of macro ‘TRASH’ 284 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 285 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:3: note: in expansion of macro ‘TRASH’ 291 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:3: note: in expansion of macro ‘TRASH’ 305 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:3: note: in expansion of macro ‘TRASH’ 307 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:3: note: in expansion of macro ‘TRASH’ 311 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:3: note: in expansion of macro ‘TRASH’ 313 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:3: note: in expansion of macro ‘TRASH’ 318 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 319 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:3: note: in expansion of macro ‘TRASH’ 320 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:3: note: in expansion of macro ‘TRASH’ 328 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 329 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:3: note: in expansion of macro ‘TRASH’ 330 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:3: note: in expansion of macro ‘TRASH’ 354 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(vertex, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:3: note: in expansion of macro ‘TRASH’ 356 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:3: note: in expansion of macro ‘TRASH’ 357 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(access, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:3: note: in expansion of macro ‘TRASH’ 359 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:3: note: in expansion of macro ‘TRASH’ 360 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 361 | fread(normal, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:3: note: in expansion of macro ‘TRASH’ 362 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:5: note: in expansion of macro ‘TRASH’ 371 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 372 | fread(triangle, 3 * sizeof(int), ntriangles, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:5: note: in expansion of macro ‘TRASH’ 373 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:5: note: in expansion of macro ‘TRASH’ 374 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 375 | fread(properties, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:5: note: in expansion of macro ‘TRASH’ 394 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 395 | fread(striangle, sizeof(short), 3 * ntriangles, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:5: note: in expansion of macro ‘TRASH’ 396 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:5: note: in expansion of macro ‘TRASH’ 397 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 398 | fread(properties, sizeof(float), 3 * nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_options’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1422:5: warning: ‘__strncat_chk’ output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] 1422 | strncat(data->basis_string, &data->gbasis[3], 1); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1411:5: warning: ‘__strncat_chk’ output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] 1411 | strncat(data->basis_string, &data->gbasis[2], 1); | ^ [ 9%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function ‘void* open_grid_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fread(&dataBegin, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] 133 | static void strnwscpy(char *target, const char *source, const int len) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp [ 10%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/hash.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/hash.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/hash.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/hash.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/hash.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_input_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1682:5: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] 1682 | strncpy(atm->type, atname, sizeof(atm->type)); | ^ [ 11%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/inthash.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/inthash.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/inthash.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/inthash.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/inthash.c In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘int mdio_readline(md_file*, char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 426 | fgets(buf, n, mf->f); | ~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 11%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_contrl’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1981:3: warning: ‘strncpy’ specified bound 8192 equals destination size [-Wstringop-truncation] 1981 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_proc_mem.isra.0’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1279:5: warning: ‘strncpy’ output may be truncated copying 256 bytes from a string of length 8191 [-Wstringop-truncation] 1279 | strncpy(data->memory,&word[2][0],sizeof(data->memory)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1272:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 1272 | strncpy(data->memory,trimright(temp),sizeof(data->memory)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_contrl_firefly’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1818:3: warning: ‘strncpy’ specified bound 8192 equals destination size [-Wstringop-truncation] 1818 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘g96_header(md_file*, char*, int, float*) [clone .constprop.0]’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:650:39: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 500 [-Wstringop-truncation] 650 | if (title && titlelen) strncpy(title, buf, titlelen); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘gro_header(md_file*, char*, int, float*, int*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1018:33: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 500 [-Wstringop-truncation] 1018 | if (title && titlelen) strncpy(title, buf, titlelen); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp: In function ‘open_gro_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:103:12: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 80 [-Wstringop-truncation] 103 | strncpy(gmx->meta->title, mdh.title, 80); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘get_traj_frame.isra.0’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:819:5: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 10 [-Wstringop-truncation] 819 | strncpy((*atoms)[i].type, (*atoms)[indexmap[i]].type, 10); | ^ [ 11%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp [ 12%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp [ 12%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:278:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 278 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 319 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 357 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:223:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 223 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:241:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘void* open_mdf_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:164:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 164 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:176:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 176 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 13%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 275 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 289 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_bonds_aux(void*, int*, int**, int**, float**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 199 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 209 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fgets(line, LINESIZE, mol2->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘void* open_mol2_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 74 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets(line, LINESIZE, fd); // Read and ignore the mol_name | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fgets(line, LINESIZE, fd); // Read the molecule info | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | fgets(line, LINESIZE, fd); // Read and ignore the mol_type | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(line, LINESIZE, fd); // Read the charge_type | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function ‘int {anonymous}::write_structure(void*, int, const molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1904:9: warning: unused variable ‘last_ctnumber’ [-Wunused-variable] 1904 | int last_ctnumber = -1; | ^~~~~~~~~~~~~ [ 13%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_rundata’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:596:25: warning: variable ‘hessian_data’ set but not used [-Wunused-but-set-variable] 596 | molfile_qm_hessian_t *hessian_data; | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘count_orbitals’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1165:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1165 | fscanf(data->file, " Ene= %f\n", &orbenergy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1166 | fscanf(data->file, " Spin= %s\n", spin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1167 | fscanf(data->file, " Occup= %f\n", &occu); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 840 | fgets(readbuf, 1024, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘open_molden_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:224:11: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 224 | fscanf(data->file, "%d", &natm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] 1097 | static void whereami(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] 1077 | static void thisline(FILE *file) { | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] 1006 | static int have_keyline(FILE *file, const char *keystring1, | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] 711 | static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] 585 | static void print_matrix4(const float mat[16]) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] 507 | static void del_wavefunction(qm_timestep_t *ts) { | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] 490 | static void replace_wavefunction(qm_timestep_t *ts, int n) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] 109 | static float get_pte_vdw_radius(const int idx) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] 102 | static float get_pte_mass(const int idx) | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] 95 | static const char *get_pte_label(const int idx) | ^~~~~~~~~~~~~ [ 13%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:350:7: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 350 | strncpy(atom->type, atname, sizeof(atom->type)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:351:7: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 351 | strncpy(atom->name, atname, sizeof(atom->name)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:317:7: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 317 | strncpy(atom->name, atname, sizeof(atom->name)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:326:7: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 1023 [-Wstringop-truncation] 326 | strncpy(data->atoms[i].type, atname, sizeof(data->atoms[i].type)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:91:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 116 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 132 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 161 | fgets(line, 80, infile); //one more read to keep us in sync | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 170 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 217 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 256 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(sub, "%03x/", i); | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:22: note: directive argument in the range [0, 2147483646] 714 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: In function ‘sprintf’, inlined from ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:9: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 722 | sprintf(subsub, "%03x", j); | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:29: note: directive argument in the range [0, 2147483646] 722 | sprintf(subsub, "%03x", j); | ^~~~~~ In function ‘sprintf’, inlined from ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:13: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp [ 14%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘read_next_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable ‘numatoms’ set but not used [-Wunused-but-set-variable] 103 | int i, numatoms; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘open_namdbin_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:78:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fread(&filen, sizeof(namdbin_int32), 1, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c.o [ 15%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned long, unsigned long, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:35: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 675 | sprintf(answer, "%03x/", d1); | ^ In function ‘sprintf’, inlined from ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:13, inlined from ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned long, unsigned long, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:779:23: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned long, unsigned long, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 673 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’, inlined from ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned long, unsigned long, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:779:23: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:29: note: directive argument in the range [0, 2147483646] 673 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:13, inlined from ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned long, unsigned long, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:779:23: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function ‘int read_parm7_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:80:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | fgets(buf, 85, file); | ~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atoms(const char*, int, molfile_atom_t*, FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:204:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | fgets(buf, 85, file); | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atype(const char*, int, molfile_atom_t*, FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:257:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 257 | fgets(buf, 85, file); | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_resnames(const char*, int, char*, FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:275:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 275 | fgets(buf, 85, file); | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_respointers(const char*, int, molfile_atom_t*, int, const char*, FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:289:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 289 | fscanf(file, " %d", &cur); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘parm7struct* read_parm7_header(FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:368:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 368 | fgets(sdum, 512, file); | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:371:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf(file, "%s\n", sdum); // "%FLAG" | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:378:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 378 | fscanf(file, "%s\n", sdum); // "TITLE" or "CTITLE" | ~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:385:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 385 | fscanf(file, "%s\n", sdum); // "FORMAT (20a4)" | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:399:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 399 | fgets(prm->title, sizeof(prm->title), file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:427:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 427 | fgets(sdum, sizeof(sdum), file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:439:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 439 | fscanf(file,parm7, | ~~~~~~^~~~~~~~~~~~ 440 | &prm->Natom, &prm->Ntypes, &prm->Nbonh, &prm->Nbona, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 441 | &prm->Ntheth, &prm->Ntheta, &prm->Nphih, &prm->Nphia, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 | &prm->Jparm, &prm->Nparm); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:443:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 443 | fscanf(file, parm7, | ~~~~~~^~~~~~~~~~~~~ 444 | &prm->Nnb, &prm->Nres, &prm->Mbona, &prm->Mtheta, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | &prm->Mphia, &prm->Numbnd, &prm->Numang, &prm->Mptra, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 | &prm->Natyp, &prm->Nphb); | ~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:447:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 447 | fscanf(file, parm7, &prm->Ifpert, &prm->Nbper, &prm->Ngper, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 | &prm->Ndper, &prm->Mbper, &prm->Mgper, &prm->Mdper, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 449 | &prm->IfBox, &prm->Nmxrs, &prm->IfCap); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:451:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 451 | fscanf(file,"%8d",&prm->Numextra); //BB | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int read_parm7_flag(FILE*, const char*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fscanf(file, "%s\n", buf); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:87:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(file, "%s\n", buf); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:97:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(file, "%s\n", buf); | ~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function ‘int {anonymous}::ReadPARM::readparm(FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | fscanf(file, " " DBLFMT, &prm->Charges[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 444 | fscanf(file, " " DBLFMT, &prm->Masses[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 510 | fscanf(file, " " DBLFMT, &prm->Rk[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 517 | fscanf(file, " " DBLFMT, &prm->Req[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 524 | fscanf(file, " " DBLFMT, &prm->Tk[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 531 | fscanf(file, " " DBLFMT, &prm->Teq[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 538 | fscanf(file, " " DBLFMT, &prm->Pk[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 545 | fscanf(file, " " DBLFMT, &prm->Pn[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fscanf(file, " " DBLFMT, &prm->Phase[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 559 | fscanf(file, " " DBLFMT, &prm->Solty[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 567 | fscanf(file, " " DBLFMT, &prm->Cn1[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 575 | fscanf(file, " " DBLFMT, &prm->Cn2[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 756 | fscanf(file, " " DBLFMT, &prm->HB12[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 763 | fscanf(file, " " DBLFMT, &prm->HB6[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 771 | fscanf(file, " " DBLFMT, &H[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:853:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fscanf(file, " " DBLFMT " " DBLFMT " " DBLFMT, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 854 | &prm->Box[0], &prm->Box[1], &prm->Box[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:867:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 867 | fscanf(file, " %d " DBLFMT " " DBLFMT " " DBLFMT " " DBLFMT, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 868 | &prm->Natcap, &prm->Cutcap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 869 | &prm->Xcap, &prm->Ycap, &prm->Zcap); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘read_parm7_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:277:12: warning: ‘__strncpy_chk’ output may be truncated copying 4 bytes from a string of length 84 [-Wstringop-truncation] 277 | strncpy(resnames, buf+4*j, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:259:12: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 84 [-Wstringop-truncation] 259 | strncpy(atom->type, buf+4*j, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:206:12: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 84 [-Wstringop-truncation] 206 | strncpy(atom->name, buf+4*j, 4); | ^ [ 16%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp [ 16%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘read_next_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:119:3: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 82 [-Wstringop-truncation] 119 | strncpy(tmp, record, PDB_RECORD_LENGTH); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:144:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 52 [-Wstringop-truncation] 144 | strncpy(numstr, record + 30, 8); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:149:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 44 [-Wstringop-truncation] 149 | strncpy(numstr+10, record + 38, 8); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:154:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 36 [-Wstringop-truncation] 154 | strncpy(numstr+20, record + 46, 8); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: ‘strncpy’ output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] 159 | strncpy(numstr+30, record + 54, 6); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: ‘strncpy’ output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] 164 | strncpy(numstr+40, record + 60, 6); | ^ [ 17%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function ‘(anonymous namespace)::read_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1786:22: warning: ‘strncpy’ specified bound 16 equals destination size [-Wstringop-truncation] 1786 | strncpy( ct.particles[to].type, v->second.funct.c_str(), | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int getUniqueResID(char*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable ‘i’ [-Wunused-variable] 443 | int i, uid; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable ‘j’ [-Wunused-variable] 484 | int i, count, atomdata, pos, idx, xyzcount, j; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable ‘oldChain’ [-Wunused-variable] 503 | char oldChain[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readAngleBonds(molfile_atom_t*, pdbxParser*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable ‘bondTable’ [-Wunused-variable] 803 | int bondTable[32]; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable ‘j’ [-Wunused-variable] 807 | int i, pos, j, k; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable ‘modelNum’ [-Wunused-variable] 811 | char modelNum[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable ‘atom’ [-Wunused-variable] 822 | molfile_atom_t * atom; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable ‘test’ [-Wunused-variable] 884 | int test = parser->nbonds + bnum; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readRMSDBonds(molfile_atom_t*, pdbxParser*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable ‘bondTable’ [-Wunused-variable] 984 | int bondTable[32]; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable ‘j’ [-Wunused-variable] 988 | int i, pos, j, k; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable ‘modelNum’ [-Wunused-variable] 991 | char modelNum[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable ‘atom’ [-Wunused-variable] 1002 | molfile_atom_t * atom; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘read_pdb_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:299:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 70 [-Wstringop-truncation] 299 | strncpy(name, record + 12, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:304:3: warning: ‘strncpy’ output may be truncated copying 1 byte from a string of length 66 [-Wstringop-truncation] 304 | strncpy(altloc, record + 16, 1); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:308:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 65 [-Wstringop-truncation] 308 | strncpy(resname, record + 17, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:317:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 60 [-Wstringop-truncation] 317 | strncpy(resid, record + 22, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: ‘strncpy’ output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] 159 | strncpy(numstr+30, record + 54, 6); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: ‘strncpy’ output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] 164 | strncpy(numstr+40, record + 60, 6); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:330:5: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 10 [-Wstringop-truncation] 330 | strncpy(segname, record + 72, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:339:5: warning: ‘strncpy’ output may be truncated copying 2 bytes from a string of length 6 [-Wstringop-truncation] 339 | strncpy(elementsymbol, record + 76, 2); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘void* open_file_write(const char*, const char*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable ‘fd’ [-Wunused-variable] 1409 | FILE* fd; | ^~ [ 17%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:313:14: warning: ‘float stringToFloat(char*)’ defined but not used [-Wunused-function] 313 | static float stringToFloat(char * str) { | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘const char* get_pte_label(int)’ defined but not used [-Wunused-function] 95 | static const char *get_pte_label(const int idx) | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘open_pdb_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] 190 | strncpy(date, record + 50, 9); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] 200 | strncpy(pdbcode, record + 62, 4); | ^ [ 18%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp: In function ‘read_phi_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp:216:14: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 84 [-Wstringop-truncation] 216 | strncpy(currNum, currChar, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘int read_plt_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 18%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In member function ‘(anonymous namespace)::SitesArray::insert_row(std::vector, std::allocator >, std::allocator, std::allocator > > > const&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:784:16: warning: ‘strncpy’ specified bound 32 equals destination size [-Wstringop-truncation] 784 | strncpy(arr, value.substr(1,value.size()-2).c_str(), N); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:786:16: warning: ‘strncpy’ specified bound 32 equals destination size [-Wstringop-truncation] 786 | strncpy(arr, value.c_str(), N); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘void* open_plt_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fread(intHeader, sizeof(int), 5, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fread(floatHeader, sizeof(float), 6, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 18%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘get_atom_radius’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 166 | char *name, *type; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable ‘name’ set but not used [-Wunused-but-set-variable] 166 | char *name, *type; | ^~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void put_element_ply(PlyFile*, void*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable ‘i’ [-Wunused-variable] 459 | int i,j,k; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void ascii_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable ‘i’ [-Wunused-variable] 1407 | int i,j,k; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable ‘i’ [-Wunused-variable] 1541 | int i,j,k; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:107:17: warning: variable ‘vert_other’ set but not used [-Wunused-but-set-variable] 107 | PlyOtherProp *vert_other=NULL; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:108:17: warning: variable ‘face_other’ set but not used [-Wunused-but-set-variable] 108 | PlyOtherProp *face_other=NULL; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1629 | fread (&len, sizeof(int), 1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘read_pqr_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:109:3: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 81 [-Wstringop-truncation] 109 | strncpy(tmp, record, PQR_RECORD_LENGTH); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1631 | fread (str, len, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void get_binary_item(FILE*, int, int*, unsigned int*, double*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2057 | fread (ptr, 1, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2063 | fread (ptr, 1, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2069 | fread (ptr, 2, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2075 | fread (ptr, 2, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2081 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2087 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2093 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2099 | fread (ptr, 8, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ [ 19%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘read_pqr_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:137:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 68 [-Wstringop-truncation] 137 | strncpy(name, record+12, 4); name[4] = 0; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:138:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 63 [-Wstringop-truncation] 138 | strncpy(resname, record+17, 4); resname[4] = 0; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:139:3: warning: ‘strncpy’ output may be truncated copying 1 byte from a string of length 59 [-Wstringop-truncation] 139 | strncpy(chain, record+21, 1); chain[1] = 0; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:140:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 58 [-Wstringop-truncation] 140 | strncpy(resid, record+22, 4); resid[4] = 0; | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] 110 | static void swap4_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: ‘fortread_4’ defined but not used [-Wunused-function] 103 | static int fortread_4(void *dest, int n, int swap, FILE *fd) { | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘fort_get_endian_reclen’ defined but not used [-Wunused-function] 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘fort_eat_recmark’ defined but not used [-Wunused-function] 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘swap8_aligned’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In member function ‘(anonymous namespace)::PseudoArray::insert_row(std::vector, std::allocator >, std::allocator, std::allocator > > > const&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:784:16: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 784 | strncpy(arr, value.substr(1,value.size()-2).c_str(), N); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:786:16: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 786 | strncpy(arr, value.c_str(), N); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In member function ‘(anonymous namespace)::AtomArray::insert_row(std::vector, std::allocator >, std::allocator, std::allocator > > > const&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:886:16: warning: ‘strncpy’ specified bound 16 equals destination size [-Wstringop-truncation] 886 | strncpy( a.name, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘recreate_command_line’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1334:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1334 | line[0] = '\0'; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1333:26: note: destination object of size 0 allocated by ‘malloc’ 1333 | line = (char *) malloc (sizeof(char) * len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘ascii_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1520:14: warning: ‘other_data’ may be used uninitialized [-Wmaybe-uninitialized] 1520 | item = elem_data + prop->offset; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1423:9: note: ‘other_data’ was declared here 1423 | char *other_data; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘binary_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1643:14: warning: ‘other_data’ may be used uninitialized [-Wmaybe-uninitialized] 1643 | item = elem_data + prop->offset; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1555:9: note: ‘other_data’ was declared here 1555 | char *other_data; | ^~~~~~~~~~ [ 19%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function ‘open_rst_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable ‘timesteprst’ set but not used [-Wunused-but-set-variable] 48 | double timesteprst; | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:67:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67 | fgets(title, 82, fd); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | fgets(line, 82, fd); | ^~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN 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-ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp [ 20%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function ‘int read_spider_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 286 | fread(datablock, total * sizeof(float), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 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-Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp [ 21%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c [ 21%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c: In function ‘read_tinker_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:103:5: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 103 | strncpy(atom->name, buffer, sizeof(atom->name)); | ^ [ 22%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 224 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 174 | for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 180 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘open_vasp5xdatcar_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 77 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 171 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:22: warning: variable ‘o’ set but not used [-Wunused-but-set-variable] 90 | float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:28: warning: variable ‘s’ set but not used [-Wunused-but-set-variable] 90 | float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘int read_uhbd_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:254:66: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 254 | if (fread(datablock + z*xysize, sizeof(float), xysize, fd) != xysize) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fread(&headersize, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 22%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_data’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_metadata’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘open_vaspchgcar_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 239 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 242 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘open_vaspoutcar_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:87:10: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_data’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 238 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_metadata’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘open_vaspparchg_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c [ 24%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘write_vaspposcar_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:360:40: warning: argument to ‘sizeof’ in ‘strncpy’ call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] 360 | strncpy(tmptype, atom->type, sizeof(atom->type)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 246 | for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 249 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 256 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_timestep’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:283:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 283 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 195 | for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 198 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 203 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:228:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 228 | for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:233:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 233 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:237:32: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:252:44: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 252 | for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘open_vaspposcar_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘open_vaspxdatcar_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:89:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fgets(lineptr, LINESIZE, poscar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:92:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, poscar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:97:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fgets(lineptr, LINESIZE, poscar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:111:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fgets(lineptr, LINESIZE, poscar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:121:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 121 | fgets(lineptr, LINESIZE, poscar); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 24%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘read_vaspxml_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:139:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:144:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 144 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘open_vaspxml_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:86:8: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:92:8: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 24%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c [ 25%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp [ 25%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 288 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 365 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 387 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 395 | fgets(nextline, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 455 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 250 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘void* open_xbgf_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function ‘vtf_read_bonds’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:147:48: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 147 | sprintf(message, "vtfplugin:%d: error: %s: \"%s\"\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function ‘vtf_open_file_read’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:538:9: warning: ‘__strncat_chk’ output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] 538 | strncat(msg, keyword, 200); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:276:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] 276 | int x, y, z, xsize, ysize, zsize, xysize, total; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data_ex(void*, molfile_volumetric_readwrite_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:338:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] 338 | int x, y, z, xsize, ysize, zsize, xysize, total; | ^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:629:7: warning: ‘__strncat_chk’ output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] 629 | strncat(msg, keyword, 200); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:371:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:306:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:72: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include/vmdconio.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include/vmdconio.h:56:12: warning: ‘int vmdcon_printf(int, const char*, ...)’ defined but not used [-Wunused-function] 56 | static int vmdcon_printf(int lvl, const char *fmt, ...) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘open_vtk_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:152:10: warning: ‘strncpy’ output may be truncated copying 256 bytes from a string of length 2039 [-Wstringop-truncation] 152 | strncpy(vtk->title, inbuf, sizeof(vtk->title) - 1); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘read_xbgf_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:143:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 223 [-Wstringop-truncation] 143 | strncpy(numstr, record + 32, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:148:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 213 [-Wstringop-truncation] 148 | strncpy(numstr+10, record + 42, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:153:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 203 [-Wstringop-truncation] 153 | strncpy(numstr+20, record + 52, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:143:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 223 [-Wstringop-truncation] 143 | strncpy(numstr, record + 32, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:148:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 213 [-Wstringop-truncation] 148 | strncpy(numstr+10, record + 42, 10); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:153:12: warning: ‘strncpy’ output may be truncated copying 10 bytes from a string of length 203 [-Wstringop-truncation] 153 | strncpy(numstr+20, record + 52, 10); | ^ [ 26%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp [ 26%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘read_xbgf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:172:10: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 241 [-Wstringop-truncation] 172 | strncpy(name, record + 14, 5); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:177:10: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 235 [-Wstringop-truncation] 177 | strncpy(resname, record + 20, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:182:10: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 154 [-Wstringop-truncation] 182 | strncpy(segname, record + 101, 4); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:197:10: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 192 [-Wstringop-truncation] 197 | strncpy(type, record+63, 5); | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object CMakeFiles/_cmd.dir/layer0/Bezier.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Bezier.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Bezier.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Bezier.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Bezier.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c: In function ‘read_xyz_structure’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:133:7: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 133 | strncpy(atom->name, buffer, sizeof(atom->name)); | ^ [ 27%] Building CXX object CMakeFiles/_cmd.dir/layer0/Block.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Block.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Block.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Block.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Block.cpp [ 27%] Building CXX object CMakeFiles/_cmd.dir/layer0/CarveHelper.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/CarveHelper.cpp.o -MF CMakeFiles/_cmd.dir/layer0/CarveHelper.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/CarveHelper.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void eatline(FILE*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:238:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 238 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void* open_xsf_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:408:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 408 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:442:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 442 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:444:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 444 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:446:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 446 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:448:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 448 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:450:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 450 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:473:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 473 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:508:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 508 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘read_xsf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:597:20: warning: ‘strncpy’ output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 597 | strncpy(atom->name, buffer, sizeof(atom->name)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘open_xsf_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:438:22: warning: ‘strncpy’ output may be truncated copying 255 bytes from a string of length 255 [-Wstringop-truncation] 438 | strncpy(set->dataname, readbuf, 255); | ^ [ 27%] Building CXX object CMakeFiles/_cmd.dir/layer0/ContourSurf.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ContourSurf.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ContourSurf.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ContourSurf.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ContourSurf.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.cpp:8: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.h: In constructor ‘CarveHelper::CarveHelper(PyMOLGlobals*, float, const float*, std::size_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.h:23:9: warning: ‘CarveHelper::m_cutoff’ will be initialized after [-Wreorder] 23 | float m_cutoff; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.h:22:16: warning: ‘const float* CarveHelper::m_vertices’ [-Wreorder] 22 | const float* m_vertices; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/CarveHelper.cpp:20:1: warning: when initialized here [-Wreorder] 20 | CarveHelper::CarveHelper(PyMOLGlobals* G, float cutoff, const float* vertices, | ^~~~~~~~~~~ [ 28%] Building CXX object CMakeFiles/_cmd.dir/layer0/Crystal.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Crystal.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Crystal.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Crystal.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Crystal.cpp [ 28%] Building CXX object CMakeFiles/_cmd.dir/layer0/Err.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Err.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Err.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Err.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Err.cpp [ 29%] Building CXX object CMakeFiles/_cmd.dir/layer0/Feedback.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Feedback.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Feedback.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Feedback.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.cpp [ 29%] Building CXX object CMakeFiles/_cmd.dir/layer0/Field.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/File.cpp.o -MF CMakeFiles/_cmd.dir/layer0/File.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/File.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/File.cpp [ 30%] Building CXX object CMakeFiles/_cmd.dir/layer0/GFXManager.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/GFXManager.cpp.o -MF CMakeFiles/_cmd.dir/layer0/GFXManager.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/GFXManager.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GFXManager.cpp [ 30%] Building CXX object CMakeFiles/_cmd.dir/layer0/GenericBuffer.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/GenericBuffer.cpp.o -MF CMakeFiles/_cmd.dir/layer0/GenericBuffer.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/GenericBuffer.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp [ 31%] Building CXX object CMakeFiles/_cmd.dir/layer0/GraphicsUtil.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/GraphicsUtil.cpp.o -MF CMakeFiles/_cmd.dir/layer0/GraphicsUtil.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/GraphicsUtil.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GraphicsUtil.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Field.cpp: In function ‘PyObject* FieldAsNumPyArray(CField*, short int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Field.cpp:83:1: warning: label ‘ok_except1’ defined but not used [-Wunused-label] 83 | ok_except1: | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Field.cpp: In function ‘CField* FieldNewFromPyList(PyMOLGlobals*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Field.cpp:179:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 179 | ok = ok && I->size() == size; | ~~~~~~~~~~^~~~~~~ [ 31%] Building CXX object CMakeFiles/_cmd.dir/layer0/Isosurf.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Isosurf.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Isosurf.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Isosurf.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Isosurf.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp: In destructor ‘virtual GenericBuffer::~GenericBuffer()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp:208:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 208 | for (auto i = 0; i < m_desc.size(); ++i) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp: In member function ‘bool GenericBuffer::sepBufferData()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp:275:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | for (auto i = 0; i < m_desc.size(); ++i) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp: In member function ‘void VertexBuffer::bind(GLuint, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp:427:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 427 | for (auto i = 0; i < m_desc.size(); ++i) { | ~~^~~~~~~~~~~~~~~ [ 31%] Building CXX object CMakeFiles/_cmd.dir/layer0/Map.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Match.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Match.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Match.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Match.cpp [ 32%] Building CXX object CMakeFiles/_cmd.dir/layer0/Matrix.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Matrix.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Matrix.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Matrix.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Matrix.cpp [ 32%] Building CXX object CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o -MF CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp [ 33%] Building CXX object CMakeFiles/_cmd.dir/layer0/MemoryUsage.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/MemoryUsage.cpp.o -MF CMakeFiles/_cmd.dir/layer0/MemoryUsage.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/MemoryUsage.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp: In function ‘void* VLADeleteRaw(void*, int, unsigned int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp:218:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | if(index < -old_size) | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp:230:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | (index < vla->size) && ((count + index) <= vla->size)) { | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp: In function ‘void* VLAInsertRaw(void*, int, unsigned int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp:251:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 251 | if(index < -old_size) | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp:258:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 258 | if(index > old_size) | ~~~~~~^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp:261:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | if((index >= 0) && (count > 0) && (index <= old_size)) { | ~~~~~~^~~~~~~~~~~ [ 33%] Building CXX object CMakeFiles/_cmd.dir/layer0/MyPNG.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/MyPNG.cpp.o -MF CMakeFiles/_cmd.dir/layer0/MyPNG.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/MyPNG.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MyPNG.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp: In function ‘size_t pymol::memory_usage()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp:38:21: warning: use of assignment suppression and length modifier together in gnu_scanf format [-Wformat=] 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp:38:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/Parse.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Parse.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Parse.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Parse.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Parse.cpp [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Pixmap.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MyPNG.cpp: In function ‘int MyPNGWrite(pymol::zstring_view, const pymol::Image&, float, int, int, float, float, png_outbuf_t*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MyPNG.cpp:300:20: warning: comparison of integer expressions of different signedness: ‘png_uint_32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 300 | for(k = 0; k < height; k++) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MyPNG.cpp:341:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 341 | for(b = 0; b < height; b++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MyPNG.cpp:342:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 342 | for(a = 0; a < width; a++) { | ~~^~~~~~~ [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/PostProcess.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/PostProcess.cpp.o -MF CMakeFiles/_cmd.dir/layer0/PostProcess.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/PostProcess.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/PostProcess.cpp [ 35%] Building CXX object CMakeFiles/_cmd.dir/layer0/PrintUtils.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/PrintUtils.cpp.o -MF CMakeFiles/_cmd.dir/layer0/PrintUtils.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/PrintUtils.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/PrintUtils.cpp [ 35%] Building CXX object CMakeFiles/_cmd.dir/layer0/ShaderMgr.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS 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-Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ShaderMgr.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ShaderMgr.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ShaderMgr.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.cpp [ 36%] Building CXX object CMakeFiles/_cmd.dir/layer0/ShaderPreprocessor.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ShaderPreprocessor.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ShaderPreprocessor.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ShaderPreprocessor.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderPreprocessor.cpp [ 36%] Building CXX object CMakeFiles/_cmd.dir/layer0/ShaderPrg.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ShaderPrg.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ShaderPrg.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ShaderPrg.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderPrg.cpp [ 36%] Building CXX object CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Sphere.cpp [ 37%] Building CXX object CMakeFiles/_cmd.dir/layer0/TTT.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/TTT.cpp.o -MF CMakeFiles/_cmd.dir/layer0/TTT.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/TTT.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TTT.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.cpp:21: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderPrg.cpp:20: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 37%] Building CXX object CMakeFiles/_cmd.dir/layer0/Tetsurf.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 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-mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Tetsurf.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Tetsurf.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Tetsurf.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Tetsurf.cpp [ 37%] Building CXX object CMakeFiles/_cmd.dir/layer0/Texture.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 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-fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Texture.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Texture.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Texture.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Texture.cpp [ 38%] Building CXX object CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Tracker.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Texture.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 38%] Building CXX object CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Triangle.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Texture.cpp: In function ‘bool TextureIsCharTextured(PyMOLGlobals*, int, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Texture.cpp:130:9: warning: unused variable ‘use_shader’ [-Wunused-variable] 130 | short use_shader = (short) SettingGetGlobal_b(G, cSetting_use_shaders); | ^~~~~~~~~~ [ 39%] Building CXX object CMakeFiles/_cmd.dir/layer0/Util.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Util2.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Util2.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Util2.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Util2.cpp [ 39%] Building CXX object CMakeFiles/_cmd.dir/layer0/Vector.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp [ 40%] Building CXX object CMakeFiles/_cmd.dir/layer0/marching_cubes.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/marching_cubes.cpp.o -MF CMakeFiles/_cmd.dir/layer0/marching_cubes.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/marching_cubes.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt.h:49, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:39: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array2d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, Array2D&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array2d_utils.h:62:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 62 | for (int i=0; i>(std::istream&, Array3D&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array3d_utils.h:47:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 47 | for (int i=0; i>(std::istream&, Fortran_Array2D&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_fortran_array2d_utils.h:61:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 61 | for (int i=1; i<=M; i++) | ^~~ /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_fortran_array2d_utils.h:67:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 67 | A = B; | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt.h:57: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_fortran_array3d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, Fortran_Array3D&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_fortran_array3d_utils.h:65:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 65 | for (int i=1; i<=M; i++) | ^~~ /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_fortran_array3d_utils.h:70:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 70 | A = B; | ^ [ 41%] Building CXX object CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o -MF CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_gl.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp: In function ‘mc::Mesh mc::march(const Field&, float, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:517:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 517 | for (int z = 0; z < zDim; ++z) { | ~~^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:550:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 550 | for (int z = 0; z < zEnd; ++z) { | ~~^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:603:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 603 | if (z == zEnd - 1) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:608:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 608 | if (z == zEnd - 1) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp: In function ‘void mc::calculateNormals(Mesh&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:681:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 681 | for (int i = 0; i < vertexCount; ++i) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:686:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 686 | for (int i = 0; i < triangleCount; ++i) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/marching_cubes.cpp:720:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 720 | for (int i = 0; i < vertexCount; ++i) { | ~~^~~~~~~~~~~~~ [ 41%] Building CXX object CMakeFiles/_cmd.dir/layer1/Basis.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Basis.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Basis.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Basis.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Basis.cpp [ 42%] Building CXX object CMakeFiles/_cmd.dir/layer1/ButMode.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ButMode.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ButMode.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ButMode.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ButMode.cpp [ 42%] Building CXX object CMakeFiles/_cmd.dir/layer1/CGO.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/CGO.cpp.o -MF CMakeFiles/_cmd.dir/layer1/CGO.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/CGO.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ButMode.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ButMode.cpp:22: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ButMode.cpp: In function ‘void ButModeFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CButMode’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ButMode.cpp:144:3: note: in expansion of macro ‘DeleteP’ 144 | DeleteP(G->ButMode); | ^~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt.h:45: In member function ‘TNT::Array1D::set_(double*, double*, double const&)’, inlined from ‘TNT::Array1D::Array1D(int, double const&)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:119:6, inlined from ‘findBest(cePoint*, cePoint*, afp**, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:506:28: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:283:20: warning: ‘memset’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 283 | *p = a; | ~~~^~~ [ 42%] Building CXX object CMakeFiles/_cmd.dir/layer1/CGOGL.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/CGOGL.cpp.o -MF CMakeFiles/_cmd.dir/layer1/CGOGL.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/CGOGL.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGOGL.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:40: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 43%] Building CXX object CMakeFiles/_cmd.dir/layer1/CGORenderer.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/CGORenderer.cpp.o -MF CMakeFiles/_cmd.dir/layer1/CGORenderer.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/CGORenderer.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGORenderer.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘void CheckAttributesForUsage(const CGO*, AttribDataDesc&, AttribDataDesc&, CGO*, bool&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:8819:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 8819 | for (auto idx = 0; idx < attrIdx; ++idx) { | ~~~~^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘void PopulateOpsIntoStructuresForConversion(std::map&, std::map >&, AttribDataDesc&, AttribDataDesc&, int&, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:8904:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 8904 | if (attrOp->incr_vertices != vertsperpickinfo) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘CGO* CGOConvertToShader(const CGO*, AttribDataDesc&, AttribDataDesc&, int, buffer_layout, bool, int*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:9236:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9236 | for (auto idx = 0; idx < attrData.size(); ++idx) { | ~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:9251:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9251 | for (auto idx = 0; idx < attrData.size(); ++idx) { | ~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGO.cpp:9262:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9262 | for (int nxt = 0; nxt < attribOp->incr_vertices; ++nxt) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object CMakeFiles/_cmd.dir/layer1/COLLADA.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/COLLADA.cpp.o -MF CMakeFiles/_cmd.dir/layer1/COLLADA.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/COLLADA.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/COLLADA.cpp [ 44%] Building CXX object CMakeFiles/_cmd.dir/layer1/Camera.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Camera.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Camera.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Camera.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Camera.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/CGOGL.cpp:9: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/COLLADA.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 44%] Building CXX object CMakeFiles/_cmd.dir/layer1/Character.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Character.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Character.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Character.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Character.cpp [ 44%] Building CXX object CMakeFiles/_cmd.dir/layer1/Color.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Color.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Color.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Color.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Control.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Control.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Control.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Control.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Control.cpp [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘ObjectGadgetRamp* ColorGetRamp(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:178:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 178 | if (index < I->Ext.size()) { | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorExtFromPyList(PyMOLGlobals*, PyObject*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:499:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 499 | for (int a = 0; a < n_ext; ++a) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:516:15: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 516 | if (a_new == I->Ext.size()) { | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorFromPyList(PyMOLGlobals*, PyObject*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:567:44: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 567 | if (partial_restore && I->Color.size() > index) { | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:573:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 573 | if (index >= I->Color.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetIndex(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:681:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 681 | if((i < I->Color.size()) && (i >= 0)) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const char* ColorGetName(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:762:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 762 | if((index >= 0) && (index < I->Color.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:774:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 774 | if (a < I->Ext.size()) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetStatus(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:790:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 790 | if((index >= 0) && (index < I->Color.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘void ColorUpdateFromLut(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:1693:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1693 | for(i = 0; i < I->Color.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:1697:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1697 | if(index < I->Color.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const float* ColorGet(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:1806:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1806 | if((index >= 0) && (index < I->Color.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const float* ColorGetRaw(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:1833:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1833 | if((index >= 0) && (index < I->Color.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetEncoded(PyMOLGlobals*, int, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:1851:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1851 | if((index >= 0) && (index < I->Color.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Control.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitiveName(PyMOLGlobals*, const Sequence&, const char*) [with Sequence = std::vector]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:302:35: required from here 302 | return findByCaseInsensitiveName(G, G->Color->Ext, name); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:243:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 243 | for (int a = 0; a < seq.size(); ++a) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitiveName(PyMOLGlobals*, const Sequence&, const char*) [with Sequence = std::vector]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:624:38: required from here 624 | color = findByCaseInsensitiveName(G, I->Color, name); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:243:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 243 | for (int a = 0; a < seq.size(); ++a) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitivePrefix(PyMOLGlobals*, const Sequence&, const char*, int&) [with Sequence = std::vector]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:739:42: required from here 739 | int color = findByCaseInsensitivePrefix(G, I->Color, name, best); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:273:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 273 | for (int a = 0; a < seq.size(); ++a) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitivePrefix(PyMOLGlobals*, const Sequence&, const char*, int&) [with Sequence = std::vector]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:741:54: required from here 741 | int const ext_color = findByCaseInsensitivePrefix(G, I->Ext, name, best); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Color.cpp:273:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 273 | for (int a = 0; a < seq.size(); ++a) { | ~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:22: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Control.cpp: In function ‘void ControlFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CControl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Control.cpp:410:3: note: in expansion of macro ‘DeleteP’ 410 | DeleteP(G->Control); | ^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp: In function ‘ExtrudeComputeTangents(CExtrude*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp:742:13: warning: ‘MEM [(float *)_62]’ may be used uninitialized [-Wmaybe-uninitialized] 742 | *(v1++) = *(v++); /* first segment */ | ^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp:744:13: warning: ‘MEM[(float *)_62 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 744 | *(v1++) = *(v++); | ^~~~~~ [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Font.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Font.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Font.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Font.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Font.cpp [ 46%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUT.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontGLUT.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUT.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUT.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/FontGLUT.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp: In function ‘ExtrudeCGOSurfaceTube(CExtrude const*, CGO*, cCylCap, float const*, bool, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp:949:46: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 949 | if(color_override && (b > start) && (b < stop)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Extrude.cpp:876:14: note: ‘stop’ was declared here 876 | int start, stop; | ^~~~ [ 46%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontType.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontType.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontType.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/FontType.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/FontGLUT.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 49%] Building CXX object CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ImageUtils.cpp [ 49%] Building CXX object CMakeFiles/_cmd.dir/layer1/Movie.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Movie.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Movie.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Movie.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Movie.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/FontType.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ImageUtils.cpp: In function ‘pymol::Result PyMOLImageComposite(PyMOLGlobals*, const pymol::Image&, const pymol::Image&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ImageUtils.cpp:54:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | for (int i = 0; i < image.getSizeInBytes() / image.getPixelSize(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object CMakeFiles/_cmd.dir/layer1/Ortho.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Ortho.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Ortho.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Ortho.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Movie.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/_cmd.dir/layer1/P.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/P.cpp.o -MF CMakeFiles/_cmd.dir/layer1/P.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/P.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘void OrthoAddOutput(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:1099:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1099 | if (cc >= OrthoLineLength - 6) { /* fail safe */ | ~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘std::unique_ptr makeBgGridImage(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:1321:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1321 | for (unsigned j = 0; j != tmpImg->getHeight(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:1322:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1322 | for (unsigned i = 0; i != tmpImg->getWidth(); ++i, q += 4) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘void OrthoDoDraw(PyMOLGlobals*, const OrthoDrawInfo&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:1873:8: warning: variable ‘double_pump’ set but not used [-Wunused-but-set-variable] 1873 | auto double_pump = SettingGet(G, cSetting_stereo_double_pump_mono); | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:59: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int WrapperObjectAssignSubScript(PyObject*, PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:873:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 873 | if (strlen(valstr) > ap->maxlen) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:897:18: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 897 | if (valint == -1 && PyErr_Occurred()) | ~~~~~~~^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int PAutoBlock(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:2337:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] 2337 | if (SavedThread[a].id == id) { | ~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int PIsGlutThread()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:2363:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2363 | return (PyThread_get_thread_ident() == P_glut_thread_id); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:2471:13: warning: ‘void PLockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] 2471 | static void PLockAPIWhileBlocked(PyMOLGlobals * G) | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:2460:13: warning: ‘void PUnlockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] 2460 | static void PUnlockAPIWhileBlocked(PyMOLGlobals * G) | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:1783:13: warning: ‘void OrthoDrawFontTextureDebug(PyMOLGlobals*, CGO*)’ defined but not used [-Wunused-function] 1783 | static void OrthoDrawFontTextureDebug(PyMOLGlobals* G, CGO* orthoCGO) | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:775:13: warning: ‘void OrthoKeyCmmd(PyMOLGlobals*, unsigned char)’ defined but not used [-Wunused-function] 775 | static void OrthoKeyCmmd(PyMOLGlobals* G, unsigned char k) | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘PLabelAtomAlt(PyMOLGlobals*, AtomInfoType*, char const*, char const*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.cpp:323:12: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 323 | strncpy(label, origexpr, OrthoLineLength); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/_cmd.dir/layer1/PConv.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/PConv.cpp.o -MF CMakeFiles/_cmd.dir/layer1/PConv.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/PConv.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.cpp In file included from /usr/include/string.h:548, from /usr/include/python3.12/Python.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:24: In function ‘strcat’, inlined from ‘OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:340:13: /usr/include/bits/string_fortified.h:130:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 130 | return __builtin___strcat_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strcat’, inlined from ‘OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ortho.cpp:357:13: /usr/include/bits/string_fortified.h:130:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 130 | return __builtin___strcat_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/_cmd.dir/layer1/Picking.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Picking.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Picking.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Picking.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Picking.cpp [ 51%] Building CXX object CMakeFiles/_cmd.dir/layer1/Pop.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Pop.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Pop.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Pop.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Pop.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.cpp: In function ‘int PConvPyListToBitmask(PyObject*, int*, ov_size)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.cpp:83:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 83 | for(int i = 0; i < ll; i++) | ~~^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.cpp: In function ‘PyObject* PConvLabPosVecToPyList(const std::vector&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.cpp:1194:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1194 | for (int a = 0; a < vec.size(); a++) { | ~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Pop.cpp:22: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Pop.cpp: In function ‘void PopFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CPop’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Pop.cpp:54:3: note: in expansion of macro ‘DeleteP’ 54 | DeleteP(G->Pop); | ^~~~~~~ [ 51%] Building CXX object CMakeFiles/_cmd.dir/layer1/PyMOLObject.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/PyMOLObject.cpp.o -MF CMakeFiles/_cmd.dir/layer1/PyMOLObject.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/PyMOLObject.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp [ 52%] Building CXX object CMakeFiles/_cmd.dir/layer1/Ray.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Ray.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Ray.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Ray.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp [ 52%] Building CXX object CMakeFiles/_cmd.dir/layer1/Rep.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Rep.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Rep.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Rep.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Rep.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp: In function ‘int ObjectMotion(pymol::CObject*, MViewAction, int, int, float, float, int, float, int, int, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp:193:15: warning: ignoring return value of ‘constexpr const _Tp& std::max(const _Tp&, const _Tp&) [with _Tp = int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 193 | std::max(0, first); | ~~~~~~~~^~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_uninitialized.h:63, from /usr/include/c++/14/memory:69, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:23, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp:17: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: declared here 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ [ 52%] Building CXX object CMakeFiles/_cmd.dir/layer1/Scene.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Scene.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Scene.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Scene.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:38: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp: In function ‘void RayRender(CRay*, unsigned int*, double, float, int, unsigned int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6070:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6070 | if(x_stop > width) | ~~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6072:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6072 | if(y_stop > height) | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6153:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6153 | for(y = 0; y < height; y++) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6154:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6154 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6165:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6165 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6176:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6176 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6237:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6237 | for(y = 0; y < height; y++) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6238:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6238 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6248:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6248 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6260:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6260 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6311:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6311 | for(y = 0; y < height; y++){ | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6331:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6331 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6350:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6350 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6364:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6364 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6378:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6378 | if(x && (y < (height - 1))) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6385:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6385 | if(y && (x < (width - 1))) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6392:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6392 | if((y < (height - 1)) && (x < (width - 1))) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6392:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6392 | if((y < (height - 1)) && (x < (width - 1))) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6548:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6548 | for(y = 0; y < height; y++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:6549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6549 | for(x = 0; x < width; x++) { | ~~^~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Rep.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 53%] Building CXX object CMakeFiles/_cmd.dir/layer1/SceneMouse.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SceneMouse.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SceneMouse.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SceneMouse.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp [ 53%] Building CXX object CMakeFiles/_cmd.dir/layer1/ScenePicking.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ScenePicking.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ScenePicking.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ScenePicking.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘int SceneViewEqual(float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp:134:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 134 | for(i = 0; i < cSceneViewSize; i++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.cpp:4166:3: warning: deleting object of polymorphic class type ‘CScene’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 4166 | delete G->Scene; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp: In function ‘RayTraceThread(_CRayThreadInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:3608:39: warning: ‘hl’ may be used uninitialized [-Wmaybe-uninitialized] 3608 | compute_background_for_pixel(bkrd_uc, isOutsideInY, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 3609 | bg_image_mode, bg_image_tilesize, bg_rgb, bg_image_linear, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3610 | (unsigned char*) T->bkrd_data, T->bgWidth, T->bgHeight, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3611 | x, wr, hl, hpixelx, orig_opaque_back ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Ray.cpp:3269:9: note: ‘hl’ was declared here 3269 | float hl; | ^~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:4: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:4: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp: In function ‘void SceneClickPickBond(PyMOLGlobals*, int, int, int, const NamedPicking&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:513:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 513 | if (atIndex == LastPicked.src.index) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp: In function ‘void PickColorConverterSetRgbaBitsFromGL(PyMOLGlobals*, PickColorConverter&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:67:26: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 67 | if (currentFrameBuffer != G->ShaderMgr->defaultBackbuffer.framebuffer) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:80:26: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 80 | if (currentFrameBuffer != G->ShaderMgr->defaultBackbuffer.framebuffer) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘SceneRenderPickingMultiPick(PyMOLGlobals*, SceneUnitContext*, Multipick*, unsigned int)’, inlined from ‘SceneRenderPicking(PyMOLGlobals*, int, ClickSide, int, Picking*, int, int, Multipick*, SceneUnitContext*, unsigned int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:323:32: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:257:7: warning: ‘previous.src.index’ may be used uninitialized [-Wmaybe-uninitialized] 257 | if (pik->src.index != previous.src.index || | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp: In function ‘SceneRenderPicking(PyMOLGlobals*, int, ClickSide, int, Picking*, int, int, Multipick*, SceneUnitContext*, unsigned int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:246:11: note: ‘previous.src.index’ was declared here 246 | Picking previous; | ^~~~~~~~ [ 54%] Building CXX object CMakeFiles/_cmd.dir/layer1/SceneRay.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SceneRay.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SceneRay.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SceneRay.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRay.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp: In function ‘SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, NamedPicking const&, int, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:455:32: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 237 [-Wformat-truncation=] 455 | " You clicked %s -> (%s)\n", buffer.c_str(), name ENDFB(G); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /builddir/build/BUILD/pymol-open-source-3.1.0/include/pymol/zstring_view.h:12, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.h:4, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:1: In function ‘snprintf’, inlined from ‘SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, NamedPicking const&, int, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:454:11: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output 21 or more bytes (assuming 276) into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRay.cpp:2: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/_cmd.dir/layer1/SceneRender.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SceneRender.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SceneRender.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SceneRender.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:11: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp: In function ‘void DoRendering(PyMOLGlobals*, CScene*, GridInfo*, int, int, float*, SceneUnitContext*, float, bool, bool, SceneRenderWhich, SceneRenderOrder)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:946:32: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 946 | if (currentDrawFramebuffer == G->ShaderMgr->defaultBackbuffer.framebuffer) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:979:36: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 979 | if (currentDrawFramebuffer == G->ShaderMgr->defaultBackbuffer.framebuffer) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:1106:36: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1106 | if (currentDrawFramebuffer == | ~~~~~~~~~~~~~~~~~~~~~~~^~ 1107 | G->ShaderMgr | ~~~~~~~~~~~~ 1108 | ->defaultBackbuffer.framebuffer) { // if rendering to screen, need to | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:1130:37: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1130 | if ((currentDrawFramebuffer == G->ShaderMgr->defaultBackbuffer.framebuffer) && | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp: In function ‘void SceneInitializeViewport(PyMOLGlobals*, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneRender.cpp:1657:30: warning: comparison of integer expressions of different signedness: ‘GLint’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1657 | if (currentFrameBuffer == | ~~~~~~~~~~~~~~~~~~~^~ 1658 | G->ShaderMgr->defaultBackbuffer.framebuffer) { // if writing to screen, then | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/_cmd.dir/layer1/SceneView.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SceneView.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SceneView.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SceneView.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SceneView.cpp [ 55%] Building CXX object CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/ScrollBar.cpp [ 55%] Building CXX object CMakeFiles/_cmd.dir/layer1/Seq.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Seq.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Seq.cpp.o.d -o 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Setting.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Setting.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Setting.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp [ 56%] Building CXX object CMakeFiles/_cmd.dir/layer1/Shaker.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Shaker.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Shaker.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Shaker.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Shaker.cpp [ 56%] Building CXX object CMakeFiles/_cmd.dir/layer1/SymOp.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SymOp.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SymOp.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SymOp.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp: In member function ‘pymol::SymOp::to_string[abi:cxx11]() const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp:37:32: warning: ‘%d’ directive output may be truncated writing between 1 and 4 bytes into a region of size between 0 and 5 [-Wformat-truncation=] 37 | std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] 37 | std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5); | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.h:9, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp:7: In function ‘snprintf’, inlined from ‘pymol::SymOp::to_string[abi:cxx11]() const’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOp.cpp:37:16: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 6 and 17 bytes into a destination of size 8 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/_cmd.dir/layer1/SymOpPConv.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SymOpPConv.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SymOpPConv.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SymOpPConv.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOpPConv.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp: In function ‘int SeqFindRowCol(PyMOLGlobals*, int, int, int*, int*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:61:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) { | ~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp: In member function ‘virtual void CSeq::reshape(int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:114:28: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 114 | if(I->Row[a].ext_len > I->Size) /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp: In member function ‘virtual void CSeq::draw(CGO*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:392:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 392 | if(max_len < row->ext_len) | ~~~~~~~~^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.h:21, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:22: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp: In function ‘void SeqFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CSeq’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:731:3: note: in expansion of macro ‘DeleteP’ 731 | DeleteP(G->Seq); | ^~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/_cmd.dir/layer1/SymOpTools.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/SymOpTools.cpp.o -MF CMakeFiles/_cmd.dir/layer1/SymOpTools.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/SymOpTools.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/SymOpTools.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.cpp:717:13: warning: ‘void SeqPurgeRowVLA(PyMOLGlobals*)’ defined but not used [-Wunused-function] 717 | static void SeqPurgeRowVLA(PyMOLGlobals * G) | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingUniqueResetAll(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp:501:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 501 | for (int a = 2; a < I->entry.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp:2020:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2020 | if (SettingGetGlobal_b(G, cSetting_precomputed_lighting)) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.cpp:2022:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022 | SceneInvalidate(G); | ^~~~~~~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/_cmd.dir/layer1/Symmetry.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Symmetry.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Symmetry.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Symmetry.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.cpp [ 58%] Building CXX object CMakeFiles/_cmd.dir/layer1/Text.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 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-MT CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o -MF CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/TypeFace.cpp [ 59%] Building CXX object CMakeFiles/_cmd.dir/layer1/View.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/View.cpp.o -MF CMakeFiles/_cmd.dir/layer1/View.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/View.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/View.cpp [ 59%] Building CXX object CMakeFiles/_cmd.dir/layer1/Wizard.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Wizard.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Wizard.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Wizard.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp: In member function ‘virtual void CWizard::draw(CGO*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp:727:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 727 | else | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp:729:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 729 | drawTopEdge(); | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp: In function ‘void WizardFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CWizard’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Wizard.cpp:845:3: note: in expansion of macro ‘DeleteP’ 845 | DeleteP(G->Wizard); | ^~~~~~~ [ 59%] Building CXX object CMakeFiles/_cmd.dir/layer2/AssemblyHelpers.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/AssemblyHelpers.cpp.o -MF CMakeFiles/_cmd.dir/layer2/AssemblyHelpers.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/AssemblyHelpers.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AssemblyHelpers.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Text.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 60%] Building CXX object CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o -MF CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.cpp [ 60%] Building CXX object CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o -MF CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfoHistory.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.cpp:37: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.cpp: In function ‘bool AtomResiFromResv(char*, size_t, int, char)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.cpp:787:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 787 | return snprintf(resi, size, "%d%c", resv, inscode) < size; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.cpp:788:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 788 | return snprintf(resi, size, "%d", resv) < size; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ [ 60%] Building CXX object CMakeFiles/_cmd.dir/layer2/BondTypeHistory.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/BondTypeHistory.cpp.o -MF CMakeFiles/_cmd.dir/layer2/BondTypeHistory.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/BondTypeHistory.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/BondTypeHistory.cpp [ 61%] Building CXX object CMakeFiles/_cmd.dir/layer2/CifFile.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/CifFile.cpp.o -MF CMakeFiles/_cmd.dir/layer2/CifFile.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/CifFile.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp [ 61%] Building CXX object CMakeFiles/_cmd.dir/layer2/CifMoleculeReader.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/CifMoleculeReader.cpp.o -MF CMakeFiles/_cmd.dir/layer2/CifMoleculeReader.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/CifMoleculeReader.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp: In function ‘std::vector, std::allocator > > > pymol::integer_packing_decode(const std::vector, std::allocator > > >&, int, int, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp:585:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 585 | for (int i = 0, j = 0; i < packedInts.size(); ++i, ++j) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp: In function ‘std::vector, std::allocator > > > pymol::string_array_decode(const std::vector&, std::vector, msgpack::v2::object> >&, const std::string&, const std::vector&, std::vector, msgpack::v2::object> >&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp:668:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 668 | for (int i = 1; i < decodedOffsets.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifFile.cpp:675:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 675 | for (int i = 0; i < indices.size(); i++) { | ~~^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:24: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp: In member function ‘void seqvec_t::set(int, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:109:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | if (i > size()) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp: In member function ‘const char* seqvec_t::get(int) const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:115:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | if (i < 1 || i > size()) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp: In function ‘CoordSet** read_pdbx_struct_assembly(PyMOLGlobals*, const pymol::cif_data*, const AtomInfoType*, const CoordSet*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:801:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | while (j < c_src_len * c_it->size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object CMakeFiles/_cmd.dir/layer2/CoordSet.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/CoordSet.cpp.o -MF CMakeFiles/_cmd.dir/layer2/CoordSet.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/CoordSet.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp: In member function ‘int CoordSet::extendIndices(int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp:1599:18: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] 1599 | if (NAtIndex < nAtom) { | ~~~~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp: In function ‘void CoordSetAtomToPDBStrVLA(PyMOLGlobals*, char**, int*, const AtomInfoType*, const float*, int, const PDBInfoRec*, const double*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.cpp:1013:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 6 bytes from a string of the same length [-Wstringop-truncation] 1013 | strncpy(anisoline, "ANISOU", 6); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object CMakeFiles/_cmd.dir/layer2/DistSet.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/DistSet.cpp.o -MF CMakeFiles/_cmd.dir/layer2/DistSet.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/DistSet.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp [ 62%] Building CXX object CMakeFiles/_cmd.dir/layer2/GadgetSet.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/GadgetSet.cpp.o -MF CMakeFiles/_cmd.dir/layer2/GadgetSet.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/GadgetSet.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/GadgetSet.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:31: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h: In function ‘read_chem_comp_bond_dict(pymol::cif_data const*, bond_dict_t&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:93:12: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 93 | strncpy(s, s_, sizeof(s)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:41:12: warning: ‘strncpy’ specified bound 4 equals destination size [-Wstringop-truncation] 41 | strncpy(s, name, sizeof(halfkey_t)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:41:12: warning: ‘strncpy’ specified bound 4 equals destination size [-Wstringop-truncation] /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:93:12: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 93 | strncpy(s, s_, sizeof(s)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:41:12: warning: ‘strncpy’ specified bound 4 equals destination size [-Wstringop-truncation] 41 | strncpy(s, name, sizeof(halfkey_t)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:93:12: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 93 | strncpy(s, s_, sizeof(s)); | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h: In member function ‘bond_dict_t::get(PyMOLGlobals*, char const*, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CifBondDict.h:93:12: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/GadgetSet.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp: In function ‘int DistSetGetLabelVertex(DistSet*, int, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp:43:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 43 | if (at >= 0 && at < I->LabCoord.size()) { | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp: In member function ‘pymol::Result > DistSet::getLabelOffset(int) const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/DistSet.cpp:59:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 59 | if (atm < 0 || atm >= this->LabPos.size()) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object CMakeFiles/_cmd.dir/layer2/HydrogenAdder.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/HydrogenAdder.cpp.o -MF CMakeFiles/_cmd.dir/layer2/HydrogenAdder.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/HydrogenAdder.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp [ 63%] Building CXX object CMakeFiles/_cmd.dir/layer2/MmodTyping.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/MmodTyping.cpp.o -MF CMakeFiles/_cmd.dir/layer2/MmodTyping.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/MmodTyping.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmodTyping.cpp [ 63%] Building CXX object CMakeFiles/_cmd.dir/layer2/MmtfMoleculeReader.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/MmtfMoleculeReader.cpp.o -MF CMakeFiles/_cmd.dir/layer2/MmtfMoleculeReader.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/MmtfMoleculeReader.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp: In function ‘int ObjectMoleculeAddSeleHydrogensRefactored(ObjectMolecule*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp:286:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 286 | for (unsigned atm = 0; atm < n_atom_old; atm++) { | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp:304:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 304 | for (unsigned atm = 0; atm < n_atom_old; ++atm) { | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp:352:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 352 | for (unsigned idx = 0; idx < cs->NIndex; ++idx) { | ~~~~^~~~~~~~~~~~ [ 64%] Building CXX object CMakeFiles/_cmd.dir/layer2/Mol2Typing.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/Mol2Typing.cpp.o -MF CMakeFiles/_cmd.dir/layer2/Mol2Typing.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/Mol2Typing.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/Mol2Typing.cpp [ 64%] Building CXX object CMakeFiles/_cmd.dir/layer2/MolV3000.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/MolV3000.cpp.o -MF CMakeFiles/_cmd.dir/layer2/MolV3000.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/MolV3000.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MolV3000.cpp [ 65%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectAlignment.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectAlignment.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectAlignment.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectAlignment.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp: In function ‘ObjectMolecule* ObjectMoleculeReadMmtfStr(PyMOLGlobals*, ObjectMolecule*, const char*, int, int, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp:183:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 183 | for (int entityIndex = 0; entityIndex < container->entityListCount; ++entityIndex) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp:186:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 186 | for (int i = 0; i < entity->chainIndexListCount; ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp:240:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 240 | for (int l = 0, offset = atomIndex; l < group->bondAtomListCount / 2; ++l) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp:304:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (int l = 0; l < container->bondAtomListCount / 2; ++l) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectCGO.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectCGO.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectCGO.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectCGO.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp [ 65%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectCallback.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectCallback.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectCallback.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectCallback.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCallback.cpp [ 66%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectCurve.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectCurve.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectCurve.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectCurve.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘PyObject* ObjectCGOAllStatesAsPyList(ObjectCGO*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:54:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘int ObjectCGOAllStatesFromPyList(ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:105:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 105 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:206:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 206 | if((state >= 0) && (state < I->State.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:503:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 503 | if (!ray) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:505:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 505 | ObjectCGORenderState(G, pass, ray, I, info, sobj, color, ramp, use_shader, cgo_lighting); | ^~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:24: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.h: In copy constructor ‘ObjectCGOState::ObjectCGOState(const ObjectCGOState&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.h:28:17: warning: ‘ObjectCGOState::G’ will be initialized after [-Wreorder] 28 | PyMOLGlobals* G; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.h:27:25: warning: ‘pymol::cache_ptr ObjectCGOState::renderCGO’ [-Wreorder] 27 | pymol::cache_ptr renderCGO; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:532:1: warning: when initialized here [-Wreorder] 532 | ObjectCGOState::ObjectCGOState(const ObjectCGOState& other) | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.h:29:58: warning: ‘ObjectCGOState::hasOpaque’ will be initialized after [-Wreorder] 29 | bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.h:29:44: warning: ‘bool ObjectCGOState::cgo_lighting’ [-Wreorder] 29 | bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque; | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:532:1: warning: when initialized here [-Wreorder] 532 | ObjectCGOState::ObjectCGOState(const ObjectCGOState& other) | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromCGO(PyMOLGlobals*, ObjectCGO*, CGO*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:617:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 617 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGODefine(PyMOLGlobals*, ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:682:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 682 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:665:7: warning: variable ‘size_n’ set but not used [-Wunused-but-set-variable] 665 | int size_n; | ^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromFloatArray(PyMOLGlobals*, ObjectCGO*, float*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:740:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 740 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:6: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCallback.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘void ObjectCurveState::updateRawCGO()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:93:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 93 | for (int i = 1; i < bezierPoints.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:103:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 103 | for (int i = 0; i < bezierPoints.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:120:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 120 | if (i != bezierPoints.size() - 1) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘virtual void ObjectCurve::render(RenderInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:230:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | if (state >= m_states.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In function ‘PyObject* BezierSplineAsPyList(const pymol::BezierSpline&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:406:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 406 | for (int i = 0; i < bezPts.size(); i++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘PyObject* ObjectCurveState::asPyList() const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:415:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 415 | for (int i = 0; i < splines.size(); i++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘PyObject* ObjectCurve::statesAsPyList() const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:425:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 425 | for (int a = 0; a < m_states.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:41:13: warning: ‘void ValidateCGO(CGO&, const ObjectCurveState&, float)’ defined but not used [-Wunused-function] 41 | static void ValidateCGO( | ^~~~~~~~~~~ [ 66%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectDist.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 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-Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectDist.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectDist.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectDist.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp [ 67%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectGadget.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 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-Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectGadget.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectGadget.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectGadget.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectGadget.cpp [ 67%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectGadgetRamp.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectGadgetRamp.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectGadgetRamp.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectGadgetRamp.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectGadgetRamp.cpp [ 67%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectGroup.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectGroup.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectGroup.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectGroup.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectGroup.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘int ObjectDistMoveWithObject(ObjectDist*, ObjectMolecule*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (int i=0; iDSet.size(); i++) { | ~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘void ObjectDistUpdateExtents(ObjectDist*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | for(int a = 0; a < I->DSet.size(); a++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘PyObject* ObjectDistDSetAsPyList(ObjectDist*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:148:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 148 | for(int a = 0; a < I->DSet.size(); a++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘int ObjectDistDSetFromPyList(ObjectDist*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:165:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 165 | for(int a = 0; a < I->DSet.size(); a++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In member function ‘virtual void ObjectDist::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 241 | for(int a = 0; a < I->DSet.size(); a++) | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘void ObjectDistInvalidateRep(ObjectDist*, cRep_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:257:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 257 | for(a = 0; a < I->DSet.size(); a++) | ~~^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectGadget.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectGadgetRamp.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 68%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMap.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectMap.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectMap.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectMap.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp [ 68%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMesh.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectMesh.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectMesh.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectMesh.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp [ 68%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMolecule.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectMolecule.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectMolecule.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectMolecule.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp [ 69%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMolecule2.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectMolecule2.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectMolecule2.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectMolecule2.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:36: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapValidXtal(ObjectMap*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:134:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 134 | if((state >= 0) && (state < I->State.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapTrim(ObjectMap*, int, float*, float*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:915:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 915 | } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapDouble(ObjectMap*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:932:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 932 | } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapHalve(ObjectMap*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:947:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 947 | } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘void ObjectMapRegeneratePoints(ObjectMap*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1190:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1190 | for (i=0; iState.size();i++){ | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘PyObject* ObjectMapAllStatesAsPyList(ObjectMap*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1280:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1280 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapAllStatesFromPyList(ObjectMap*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1438:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1438 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapNewCopy(PyMOLGlobals*, const ObjectMap*, ObjectMap**, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1510:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1510 | for(state = 0; state < src->State.size(); state++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1519:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1519 | if(source_state < src->State.size()) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapState* ObjectMapStatePrime(ObjectMap*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1536 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘void ObjectMapUpdateExtents(ObjectMap*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1549:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1549 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In member function ‘virtual void ObjectMap::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:1675:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1675 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapCCP4StrToMap(ObjectMap*, char*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2298:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2298 | if(bytes < 256 * sizeof(int)) { | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2308:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2308 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2943:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2943 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapXPLORStrToMap(ObjectMap*, char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:3217:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3217 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapFLDStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:3438:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3438 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapBRIXStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:3767:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3767 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4173:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 4173 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadCCP4(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4695:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4695 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapACNTStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5246:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 5246 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadXPLOR(PyMOLGlobals*, ObjectMap*, const char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5558:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5558 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyBrick(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5713:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 5713 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyMap(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5811:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 5811 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:33: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘int ObjectMoleculeFillOpenValences(ObjectMolecule*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:3549:14: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘signed char’ [-Wsign-compare] 3549 | if((nn >= ai->valence) || (!flag)) | ~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘pymol::Result<> ObjectMoleculeAddBondByIndices(ObjectMolecule*, unsigned int, unsigned int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:4346:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 4346 | if (atm1 >= I->NAtom || atm2 >= I->NAtom) { | ~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:4346:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 4346 | if (atm1 >= I->NAtom || atm2 >= I->NAtom) { | ~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In member function ‘bool ObjectMolecule::atomHasAnyCoordinates(size_t) const’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:11774:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 11774 | for (size_t i = 0; i < NCSet; ++i) { | ~~^~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:43: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp: In function ‘bool ObjectMoleculeConnect(ObjectMolecule*, int&, pymol::vla&, CoordSet*, int, int, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:3764:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3764 | for (unsigned i = 0; i < cs->NIndex; ++i) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp: In lambda function: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:3793:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 3793 | if (i <= j && !symop) | ~~^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp: In function ‘bool ObjectMoleculeConnect(ObjectMolecule*, int&, pymol::vla&, CoordSet*, int, int, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:3898:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3898 | for (unsigned i = 0; i < cs->NIndex; ++i) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:3914:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3914 | for (unsigned a = 0; a < cs->NTmpBond; ++a) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:3964:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3964 | for (unsigned a = 0; a < cs->NTmpLinkBond; ++a) { | ~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp: In member function ‘ObjectMesh::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:508:39: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 226 [-Wformat-truncation=] 508 | "ObjectMeshUpdate-Error: map '%s' has been deleted.\n", | ^~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 50 and 305 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:541:38: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 232 [-Wformat-truncation=] 541 | " ObjectMesh: updating \"%s\".\n", I->Name ENDFB(G); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 27 and 282 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp: In function ‘ObjectMeshDump(ObjectMesh*, char const*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:333:25: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] 333 | " ObjectMeshDump: %s written to %s\n", I->Name, fname ENDFB(I->G); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output 31 or more bytes (assuming 286) into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 69%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMolecule3.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectMolecule3.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectMolecule3.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectMolecule3.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘ObjectMoleculeMOLStr2CoordSet(PyMOLGlobals*, char const*, AtomInfoType**, char const**) [clone .constprop.0]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:7597:37: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 224 [-Wformat-truncation=] 7597 | " ObjMolMOLStr2CoordSet: title '%s'\n", nameTmp ENDFB(G) | ^~ ~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:49: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 34 and 289 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:7645:16: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] 7645 | strncpy(atInfo[a].elem, cc, cElemNameLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapDump(ObjectMap const*, char const*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5984:24: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 239 [-Wformat-truncation=] 5984 | " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G); | ^~ In file included from /usr/include/stdio.h:980, from /usr/include/python3.12/Python.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:21: In function ‘snprintf’, inlined from ‘ObjectMapDump(ObjectMap const*, char const*, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5983:5: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output 30 or more bytes (assuming 285) into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp: In function ‘ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, char const*, char const*, char const*, char const*, char const*, char const*, float, int, float, float, char const*, float const*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:335:27: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] 335 | " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", | ^~ In file included from /usr/include/stdio.h:980, from /usr/include/python3.12/Python.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:24: In function ‘snprintf’, inlined from ‘ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, char const*, char const*, char const*, char const*, char const*, char const*, float, int, float, float, char const*, float const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:334:7: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 26 and 291 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘std::vector ObjectMoleculeGetMolMappingVec(const ObjectMolecule&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp:42:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 42 | for (size_t b = 0; b < objmol.NBond; ++b) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘void ObjectMoleculePBCUnwrap(ObjectMolecule&, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp:151:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 151 | for (unsigned atm = 0; atm != objmol.NAtom; ++atm) { | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘ObjectMoleculeLoadRSTFile(PyMOLGlobals*, ObjectMolecule*, char const*, int, int, char)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:1407:10: warning: ‘buffer’ may be used uninitialized [-Wmaybe-uninitialized] 1407 | mfree(buffer); /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:1304:9: note: ‘buffer’ was declared here 1304 | char *buffer, *p; | ^~~~~~ [ 70%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectSlice.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectSlice.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectSlice.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectSlice.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp [ 70%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectSurface.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectSurface.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectSurface.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectSurface.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In member function ‘ObjectMolecule::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10623:82: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] 10623 | " ObjectMolecule-DEBUG: updating representations for state %d of \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 68 and 333 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, float const*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10749:43: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] 10749 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", | ^~ 10750 | buffer, v[0], v[1], v[2], state + 1, mode, 0); | ~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10749:21: note: directive argument in the range [-2147483647, 2147483647] 10749 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10749:14: note: ‘sprintf’ output between 78 and 2036 bytes into a destination of size 1024 10749 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10750 | buffer, v[0], v[1], v[2], state + 1, mode, 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2962:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] 2962 | " PHIStrToMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2961:5, inlined from ‘ObjectMapReadPHIStr(PyMOLGlobals*, ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4804:25, inlined from ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2971:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] 2971 | " PHIStrToMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2970:5, inlined from ‘ObjectMapReadPHIStr(PyMOLGlobals*, ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4804:25, inlined from ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2977:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] 2977 | " PHIStrToMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:2976:5, inlined from ‘ObjectMapReadPHIStr(PyMOLGlobals*, ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4804:25, inlined from ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:3059:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] 3059 | " PHIStrToMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:3058:5, inlined from ‘ObjectMapReadPHIStr(PyMOLGlobals*, ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4804:25, inlined from ‘ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, char const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:33: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘PyObject* ObjectSliceAllStatesAsPyList(ObjectSlice*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:78:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 78 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:210:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for(a = 0; a < State.size(); a++) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:633:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 633 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceDrag(ObjectSlice*, int, int, float*, float*, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:679:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 679 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘int ObjectSliceGetVertex(ObjectSlice*, int, int, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:750:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 750 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::render(RenderInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:925:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 925 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:967:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 967 | if(cur_state >= I->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:981:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 981 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1226 | if(cur_state >= I->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSliceState* ObjectSliceStateGetActive(ObjectSlice*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1244:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1244 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSlice* ObjectSliceFromMap(PyMOLGlobals*, ObjectSlice*, ObjectMap*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1285:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1285 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceRecomputeExtent(ObjectSlice*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1362:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1362 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:35: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:84:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 84 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:237:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:282:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 282 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceInvalidateMapName(ObjectSurface*, const char*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:312:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 312 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ In function ‘ObjectMoleculeXYZStr2CoordSet(PyMOLGlobals*, char const*, AtomInfoType**, char const**)’, inlined from ‘ObjectMoleculeReadStr(PyMOLGlobals*, ObjectMolecule*, char const**, cLoadType_t, int, int, int, int, char*, short, _OVLexicon*)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:8569:43: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:2916:16: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] 2916 | strncpy(ai->elem, cc, cElemNameLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘ObjectSurface* ObjectSurfaceFromBox(PyMOLGlobals*, ObjectSurface*, ObjectMap*, int, int, float*, float*, float, cIsosurfaceMode, float, pymol::vla&&, cIsosurfaceSide, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:1042:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1042 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:1138:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1138 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4291:18: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] 4291 | " ObjectMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4290:3: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4291:18: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] 4291 | " ObjectMap: %s\n", cc ENDFB(I->G); | ^~ ~~ In function ‘snprintf’, inlined from ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4290:3: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘ObjectSlice::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:639:42: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 225 [-Wformat-truncation=] 639 | "ObjectSliceUpdate-Error: map '%s' has been deleted.\n", oss->MapName | ^~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:44: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 51 and 306 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:650:39: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 231 [-Wformat-truncation=] 650 | " ObjectSlice: updating \"%s\".\n", I->Name ENDFB(I->G); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 28 and 283 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘ObjectSurfaceDump(ObjectSurface*, char const*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:269:30: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] 269 | " ObjectSurfaceDump: %s written to %s\n", I->Name, fname ENDFB(I->G); | ^~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:45: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output 34 or more bytes (assuming 289) into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 70%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectVolume.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/ObjectVolume.cpp.o -MF CMakeFiles/_cmd.dir/layer2/ObjectVolume.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/ObjectVolume.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp [ 71%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepAngle.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepAngle.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepAngle.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepAngle.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepAngle.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In member function ‘ObjectSurface::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:494:43: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] 494 | " ObjectSurface: updating \"%s\".\n", I->Name ENDFB(I->G); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 30 and 285 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:38: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepAngle.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 71%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepCartoon.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepCartoon.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepCartoon.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepCartoon.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘PyObject* ObjectVolumeAllStatesAsPyList(ObjectVolume*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:133:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 133 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeAllStatesFromPyList(ObjectVolume*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:254:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 254 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeInvalidateMapName(ObjectVolume*, const char*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:319:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 319 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:347:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 347 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::update()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:408:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 408 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:446:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | for (i = 0; i < vs->Ramp.size(); i += 5) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::render(RenderInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:765:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 765 | for(a = 0; a < I->State.size(); ++a) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘ObjectVolume* ObjectVolumeFromXtalSym(PyMOLGlobals*, ObjectVolume*, ObjectMap*, CSymmetry*, int, int, float*, float*, float, int, float, float*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:1125:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1125 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘void ObjectVolumeRecomputeExtent(ObjectVolume*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:1226:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1226 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: At global scope: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:663:15: warning: ‘size_t createPreintegrationTexture(PyMOLGlobals*, const float*, int)’ defined but not used [-Wunused-function] 663 | static size_t createPreintegrationTexture(PyMOLGlobals * G, const float *Table, const int count) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepCylBond.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepCylBond.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepCylBond.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepCylBond.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCylBond.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘ObjectVolumeStateGetMapState(ObjectVolumeState*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:80:33: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] 80 | "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName | ^~ In file included from /usr/include/stdio.h:980, from /usr/include/python3.12/Python.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:20: In function ‘snprintf’, inlined from ‘ObjectVolumeStateGetMapState(ObjectVolumeState*)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:79:5: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 46 and 301 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp: In function ‘Rep* RepCartoonNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:3746:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class CCInOut’; use assignment or value-initialization instead [-Wclass-memaccess] 3746 | memset(car, 0, sizeof(*car) * nAtIndex); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:45:7: note: ‘class CCInOut’ declared here 45 | class CCInOut { | ^~~~~~~ [ 72%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepDihedral.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepDihedral.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepDihedral.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepDihedral.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDihedral.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCylBond.cpp:32: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:29: In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘ring_connector_visible(PyMOLGlobals*, AtomInfoType const*, AtomInfoType const*, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:338:23: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:25, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.h:25, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:36: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘ring_connector_visible(PyMOLGlobals*, AtomInfoType const*, AtomInfoType const*, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘ring_connector_visible(PyMOLGlobals*, AtomInfoType const*, AtomInfoType const*, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:339:23: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘ring_connector_visible(PyMOLGlobals*, AtomInfoType const*, AtomInfoType const*, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDihedral.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp: In function ‘do_ring(PyMOLGlobals*, nuc_acid_data*, int, int*, ObjectMolecule*, CoordSet*, float, CGO*, int, float, int, int, int, float, float, int*, float*, float)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1008:65: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1008 | float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSetting_cartoon_transparency, 1.0f - alpha); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:462:11: note: ‘i’ was declared here 462 | int i; | ^ [ 72%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepDistDash.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepDistDash.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepDistDash.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepDistDash.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDistDash.cpp [ 73%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepDistLabel.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepDistLabel.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepDistLabel.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepDistLabel.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDistLabel.cpp [ 73%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepDot.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepDot.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepDot.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepDot.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDistDash.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDistLabel.cpp:28: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp:32: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 73%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepEllipsoid.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepEllipsoid.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepEllipsoid.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepEllipsoid.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepEllipsoid.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/CoordSet.h:22, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.h:21, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp: In function ‘RepDotDoNew(CoordSet*, cRepDot_t, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp:463:46: warning: ‘vn’ may be used uninitialized [-Wmaybe-uninitialized] 463 | I->VN = ReallocForSure(I->VN, float, (vn - I->VN)); | ~~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepDot.cpp:263:14: note: ‘vn’ was declared here 263 | float *v, *vn; | ^~ [ 74%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepLabel.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepLabel.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepLabel.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepLabel.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepLabel.cpp [ 74%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepMesh.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepMesh.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepMesh.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepMesh.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp [ 75%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepNonbonded.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepNonbonded.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepNonbonded.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepNonbonded.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepNonbonded.cpp [ 75%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepNonbondedSphere.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepNonbondedSphere.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepNonbondedSphere.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepNonbondedSphere.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepLabel.cpp:31: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepNonbonded.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 75%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepRibbon.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepRibbon.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepRibbon.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepRibbon.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepRibbon.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp:30: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:23, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp:17: In member function ‘std::unique_ptr >::~unique_ptr()’, inlined from ‘pymol::cache_ptr >::~cache_ptr()’ at /builddir/build/BUILD/pymol-open-source-3.1.0/include/pymol/memory.h:47:7, inlined from ‘Isofield::~Isofield()’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Isosurf.h:30:8, inlined from ‘RepMeshNew(CoordSet*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp:1063:5: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: ‘field’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp: In function ‘RepMeshNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepMesh.cpp:725:13: note: ‘field’ was declared here 725 | Isofield *field; | ^~~~~ [ 76%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepSphere.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepSphere.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepSphere.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepSphere.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphere.cpp [ 76%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepSphereGenerate.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepSphereGenerate.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepSphereGenerate.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepSphereGenerate.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphereGenerate.cpp [ 77%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepSphereImmediate.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepSphereImmediate.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepSphereImmediate.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepSphereImmediate.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphereImmediate.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepRibbon.cpp: In function ‘RepRibbonNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:422:15: warning: ‘MEM [(float *)_706]’ may be used uninitialized [-Wmaybe-uninitialized] 422 | *(v1++) = *(v++); /* first segment */ | ^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:424:15: warning: ‘MEM[(float *)_706 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 424 | *(v1++) = *(v++); | ^~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphere.cpp:34: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphereImmediate.cpp:20: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSphereGenerate.cpp:20: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 77%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepSurface.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepSurface.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepSurface.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepSurface.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp [ 77%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepWireBond.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/RepWireBond.cpp.o -MF CMakeFiles/_cmd.dir/layer2/RepWireBond.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/RepWireBond.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepWireBond.cpp [ 78%] Building CXX object CMakeFiles/_cmd.dir/layer2/Sculpt.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/Sculpt.cpp.o -MF CMakeFiles/_cmd.dir/layer2/Sculpt.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/Sculpt.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/Sculpt.cpp [ 78%] Building CXX object CMakeFiles/_cmd.dir/layer2/SculptCache.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/SculptCache.cpp.o -MF CMakeFiles/_cmd.dir/layer2/SculptCache.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/SculptCache.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SculptCache.cpp [ 78%] Building CXX object CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o -MF CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp:35: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4701:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4701 | for (auto j = 0; j < edges[i].size(); j += 3) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4713:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4713 | for (auto j = 0; j < edges[i].size(); j += 3) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4724:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4724 | for (auto i = 0; i < unique_edges.size(); i += 2) { | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/Sculpt.cpp:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/RepWireBond.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:25, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.h:9, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:10: In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:57:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:25: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:55:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:49:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:47:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ [ 79%] Building CXX object CMakeFiles/_cmd.dir/layer2/VFont.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/AtomIterators.cpp.o -MF 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CMakeFiles/_cmd.dir/layer3/CifDataValueFormatter.cpp.o -MF CMakeFiles/_cmd.dir/layer3/CifDataValueFormatter.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/CifDataValueFormatter.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/CifDataValueFormatter.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/AtomIterators.cpp: In member function ‘virtual bool SeleAtomIterator::next()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/AtomIterators.cpp:65:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 65 | while ((++a) < I->Table.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/AtomIterators.cpp: In member function ‘virtual bool SeleCoordIterator::next()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/AtomIterators.cpp:133:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 133 | for (a++; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ [ 80%] Building CXX object CMakeFiles/_cmd.dir/layer3/Editor.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated 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-I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/ExecutivePython.cpp.o -MF CMakeFiles/_cmd.dir/layer3/ExecutivePython.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/ExecutivePython.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:38: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘pymol::Result<> EditorSelect(PyMOLGlobals*, const char*, const char*, const char*, const char*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:778:7: warning: variable ‘result’ set but not used [-Wunused-but-set-variable] 778 | int result = false; | ^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsosurfaceEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:990:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 990 | if(map_state >= mapObj->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsomeshEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, float)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:1136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1136 | if(map_state >= mapObj->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveVolume(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:1309:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1309 | if(map_state >= mapObj->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:1: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSmooth(PyMOLGlobals*, const char*, int, int, int, int, int, int, float, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:6186:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 6186 | for (int c = 0; c < n_atom; ++c) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveMapSet(PyMOLGlobals*, const char*, int, const char*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:6356:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 6356 | if(obj->State.size() > max_n_state) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:6467:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6467 | if(src_state < obj->State.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveRenderSelectionsFromTargets(PyMOLGlobals*, bool, int, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:8341:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 8341 | if (I->selIndicatorsCGO = optimized) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals*, pymol::zstring_view, PyObject*, pymol::zstring_view, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:171:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 171 | for(size_t c = 0; c < n_cols; ++c) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:180:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 180 | for(size_t i = 0; i < n_idx; ++i) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘float ExecutiveRMSPairs(PyMOLGlobals*, const std::vector&, int, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11154:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 11154 | for(a = 0; a < pairs; a++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11159:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 11159 | if(a < (pairs - 1)) | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveColor(PyMOLGlobals*, const char*, const char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12528:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 12528 | int ok = false; | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14196:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 14196 | for (unsigned idx = 0; idx < cs->NIndex; ++idx) { | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14223:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 14223 | for (unsigned atm = 0; atm < new_obj->NAtom; ++atm) { | ~~~~^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:52: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:100:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 100 | else \ | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14324:7: note: in expansion of macro ‘ListDelete’ 14324 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:102:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 102 | (Elem)->Link = nullptr; \ | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14324:7: note: in expansion of macro ‘ListDelete’ 14324 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:100:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 100 | else \ | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14336:7: note: in expansion of macro ‘ListDelete’ 14336 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:102:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 102 | (Elem)->Link = nullptr; \ | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14336:7: note: in expansion of macro ‘ListDelete’ 14336 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::click(int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15027:68: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15027 | if(((panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15028:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15028 | ((!panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > panel->nest_level)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::release(int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15316:65: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15316 | (((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15317:66: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15317 | ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15458:70: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15458 | if(((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15459:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15459 | ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15494:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15494 | if(!((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:27: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CExecutive’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:16446:3: note: in expansion of macro ‘DeleteP’ 16446 | DeleteP(G->Executive); | ^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSliceNew(PyMOLGlobals*, const char*, const char*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:16757:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16757 | if(map_state >= mapObj->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In instantiation of ‘ExecutiveUpdateObjectsImpl(PyMOLGlobals*, const pymol::CObject&, std::unordered_set&):: [with auto:3 = ObjectMolecule*; auto:4 = const ObjectDist*]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17125:27: required from here 17125 | if (is_mol_in_dist(mol, measure)) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17107:21: warning: loop variable ‘ds’ creates a copy from type ‘const pymol::copyable_ptr’ [-Wrange-loop-construct] 17107 | for (const auto ds : dist->DSet) { | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17107:21: note: use reference type to prevent copying 17107 | for (const auto ds : dist->DSet) { | ^~ | & /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In instantiation of ‘ExecutiveUpdateObjectsImpl(PyMOLGlobals*, const pymol::CObject&, std::unordered_set&):: [with auto:3 = const ObjectMolecule*; auto:4 = ObjectDist*]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17134:27: required from here 17134 | if (is_mol_in_dist(mol, measure)) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17107:21: warning: loop variable ‘ds’ creates a copy from type ‘const pymol::copyable_ptr’ [-Wrange-loop-construct] 17107 | for (const auto ds : dist->DSet) { | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:17107:21: note: use reference type to prevent copying 17107 | for (const auto ds : dist->DSet) { | ^~ | & In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:39: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TrackerList.h: In instantiation of ‘pymol::TrackerAdapter::TrackerAdapterIterator::TrackerAdapterIterator(CTracker*, int) [with bool IsConst = false; T = SpecRec]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TrackerList.h:99:29: required from ‘pymol::TrackerAdapter::iterator pymol::TrackerAdapter::begin() [with T = SpecRec; iterator = pymol::TrackerAdapter::TrackerAdapterIterator]’ 99 | iterator begin() { return iterator(m_tracker, m_list_id); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:204:62: required from here 204 | for (auto& rec : ExecutiveGetSpecRecsFromPattern(G, pattern)) { | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TrackerList.h:80:15: warning: ‘pymol::TrackerAdapter::TrackerAdapterIterator::m_tracker’ will be initialized after [-Wreorder] 80 | CTracker* m_tracker; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TrackerList.h:79:9: warning: ‘int pymol::TrackerAdapter::TrackerAdapterIterator::m_iter_id’ [-Wreorder] 79 | int m_iter_id = -1; | ^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/TrackerList.h:35:14: warning: when initialized here [-Wreorder] 35 | explicit TrackerAdapterIterator(CTracker* tracker, int list_id) | ^~~~~~~~~~~~~~~~~~~~~~ [ 81%] Building CXX object CMakeFiles/_cmd.dir/layer3/Interactions.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/Interactions.cpp.o -MF CMakeFiles/_cmd.dir/layer3/Interactions.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/Interactions.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Interactions.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘EditorPrepareDrag(PyMOLGlobals*, pymol::CObject*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:1935:29: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] 1935 | " Editor: grabbing (%s).", name ENDFB(G); | ^~ ~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:42: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 22 and 277 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘EditorDefineExtraPks(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:337:29: warning: ‘%s’ directive writing up to 255 bytes into a region of size 249 [-Wformat-overflow=] 337 | sprintf(buffer, "(byres %s)", name); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:337:12: note: ‘sprintf’ output between 9 and 264 bytes into a destination of size 256 337 | sprintf(buffer, "(byres %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:339:31: warning: ‘%s’ directive writing up to 255 bytes into a region of size 247 [-Wformat-overflow=] 339 | sprintf(buffer, "(bychain %s)", name); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:339:12: note: ‘sprintf’ output between 11 and 266 bytes into a destination of size 256 339 | sprintf(buffer, "(bychain %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:341:32: warning: ‘%s’ directive writing up to 255 bytes into a region of size 246 [-Wformat-overflow=] 341 | sprintf(buffer, "(byobject %s)", name); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Editor.cpp:341:12: note: ‘sprintf’ output between 12 and 267 bytes into a destination of size 256 341 | sprintf(buffer, "(byobject %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Building CXX object CMakeFiles/_cmd.dir/layer3/MaeExportHelpers.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/MaeExportHelpers.cpp.o -MF CMakeFiles/_cmd.dir/layer3/MaeExportHelpers.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/MaeExportHelpers.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Interactions.cpp: In function ‘int pymol::PrepareNeighborTables(PyMOLGlobals*, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Interactions.cpp:708:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 708 | for (int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ [ 82%] Building CXX object CMakeFiles/_cmd.dir/layer3/MoleculeExporter.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/MoleculeExporter.cpp.o -MF CMakeFiles/_cmd.dir/layer3/MoleculeExporter.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/MoleculeExporter.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MoleculeExporter.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:17: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:23, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:11: In function ‘SettingUniqueGetTypedValuePtr(PyMOLGlobals*, int, int, int, bool*)’, inlined from ‘SettingUniqueGetIfDefined(PyMOLGlobals*, int, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:472:39, inlined from ‘AtomSettingGetIfDefined(PyMOLGlobals*, AtomInfoType const*, int, bool*)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:509:33, inlined from ‘AtomSettingGetWD(PyMOLGlobals*, AtomInfoType const*, int, bool)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:519:36, inlined from ‘SettingGet(PyMOLGlobals*, SeleCoordIterator const&, int)bool’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:26:26, inlined from ‘MaeExportGetAtomStyle(PyMOLGlobals*, SeleCoordIterator const&)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:75:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Setting.h:461:11: warning: ‘out’ may be used uninitialized [-Wmaybe-uninitialized] 461 | int i = *out; | ^~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘MaeExportGetAtomStyle(PyMOLGlobals*, SeleCoordIterator const&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/AtomInfo.h:518:5: note: ‘out’ was declared here 518 | V out; | ^~~ [ 82%] Building CXX object CMakeFiles/_cmd.dir/layer3/MovieScene.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/MovieScene.cpp.o -MF CMakeFiles/_cmd.dir/layer3/MovieScene.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/MovieScene.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MovieScene.cpp [ 83%] Building CXX object CMakeFiles/_cmd.dir/layer3/PlugIOManager.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/PlugIOManager.cpp.o -MF CMakeFiles/_cmd.dir/layer3/PlugIOManager.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/PlugIOManager.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MoleculeExporter.cpp:24: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Movie.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/MovieScene.cpp:11: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In function ‘ExecutiveGetAdjustedSelectionWidth(PyMOLGlobals*, bool)’, inlined from ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:8414:50: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:8192:36: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 8192 | width = static_cast(width * 1.44f); | ~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:8180:7: note: ‘width’ was declared here 8180 | int width; | ^~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetBondSettingFromString(PyMOLGlobals*, int, char const*, char const*, char const*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11551:28: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 11551 | " Setting: %s set for %d bonds in object \"%s\".\n", | ^~ 11552 | name, nSet, obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11551:17: note: directive argument in the range [1, 2147483647] 11551 | " Setting: %s set for %d bonds in object \"%s\".\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:94: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveGetBondSetting(PyMOLGlobals*, int, char*, char const*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11632:26: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 11632 | " Getting: %s for %d bonds in object \"%s\".\n", | ^~ 11633 | name, nSet, obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11632:15: note: directive argument in the range [1, 2147483647] 11632 | " Getting: %s for %d bonds in object \"%s\".\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 38 and 556 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp: In function ‘ObjectMap* PlugIOManagerLoadVol(PyMOLGlobals*, ObjectMap*, const char*, int, int, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:411:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 411 | if(obj->State.size() <= state) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetBondSetting(PyMOLGlobals*, int, _object*, char const*, char const*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11732:62: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 208 and 217 [-Wformat-truncation=] 11732 | " Setting: %s set for %d bonds in object \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 42 or more bytes (assuming 306) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveUnsetBondSetting(PyMOLGlobals*, int, char const*, char const*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11811:26: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 11811 | " Setting: %s unset for %d bonds in object \"%s\".\n", | ^~ 11812 | name, nSet, rec->obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11811:15: note: directive argument in the range [1, 2147483647] 11811 | " Setting: %s unset for %d bonds in object \"%s\".\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 44 and 562 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetObjSettingFromString(PyMOLGlobals*, int, char const*, pymol::CObject*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12353:30: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12353 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~ 12354 | name, value2, obj->Name, state + 1 ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12353:19: note: directive argument in the range [1, 2147483647] 12353 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12345:30: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12345 | " Setting: %s set to %s in object \"%s\".\n", | ^~ 12346 | name, value2, obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12324:29: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12324 | PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSettingFromString(PyMOLGlobals*, int, char const*, char const*, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12256:36: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12256 | " Setting: %s set for %d atoms in object \"%s\".\n", | ^~ 12257 | name, op.i4, rec->obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12224:32: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12224 | " Setting: %s set to %s in %d objects, state %d.\n", | ^~ 12225 | name, value2, nObj, state + 1 ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12224:21: note: directive argument in the range [1, 2147483647] 12224 | " Setting: %s set to %s in %d objects, state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12224:21: note: directive argument in the range [1, 2147483647] /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1338 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12221:32: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12221 | " Setting: %s set to %s in %d objects.\n", name, value2, nObj ENDF(G); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12221:21: note: directive argument in the range [1, 2147483647] 12221 | " Setting: %s set to %s in %d objects.\n", name, value2, nObj ENDF(G); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1320 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12288:36: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12288 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~ 12289 | name, value2, rec->obj->Name, state + 1 ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12288:25: note: directive argument in the range [1, 2147483647] 12288 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12280:36: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12280 | " Setting: %s set to %s in object \"%s\".\n", | ^~ 12281 | name, value2, rec->obj->Name ENDF(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12184:29: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12184 | PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); | ^~ ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp: In function ‘PlugIOManagerLoad’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:941:65: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] 941 | " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); | ^~ In file included from /usr/include/stdio.h:980, from /usr/include/python3.12/Python.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:21: In function ‘snprintf’, inlined from ‘PlugIOManagerLoad’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:940:7: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 58 and 313 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object CMakeFiles/_cmd.dir/layer3/RingFinder.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/RingFinder.cpp.o -MF CMakeFiles/_cmd.dir/layer3/RingFinder.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/RingFinder.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/RingFinder.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveRemoveAtoms(PyMOLGlobals*, char const*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:9120:58: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 207 and 217 [-Wformat-truncation=] 9120 | " Remove: eliminated %d atoms in model \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 42 and 307 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/RingFinder.cpp: In member function ‘void AbstractRingFinder::recursion(int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/RingFinder.cpp:23:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23 | } else if (depth < m_indices.size() - 1) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, CSymmetry const&, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5973:46: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 199 [-Wformat-truncation=] 5973 | " %s-Warning: Cannot set symmetry for '%s' (type %s)\n", __func__, | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 84 and 339 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5982:43: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 202 [-Wformat-truncation=] 5982 | " %s-Details: Updated symmetry for '%s'\n", __func__, obj->Name ENDFB(G); | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 311 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5973:46: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 199 [-Wformat-truncation=] 5973 | " %s-Warning: Cannot set symmetry for '%s' (type %s)\n", __func__, | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 84 and 339 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 83%] Building CXX object CMakeFiles/_cmd.dir/layer3/Seeker.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/Seeker.cpp.o -MF CMakeFiles/_cmd.dir/layer3/Seeker.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/Seeker.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSpectrum(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, float, float, int, int, pymol::zstring_view, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:4786:24: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 4786 | strncpy(value_s, raw_ptr, sizeof(value_e)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:29: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerRefresh(PyMOLGlobals*, std::vector&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:485:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 485 | for(int b = 0; b < nRow; b++) { | ~~^~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:1150:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1150 | if(row->len < min_pad) { | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:1186:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1186 | if(row->len < min_pad) { | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp: In lambda function: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:1248:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1248 | for(int i = 0; i < str_size; i++){ | ~~^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:1930:27: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1930 | if(row->ext_len < stop) | ~~~~~~~~~~~~~^~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Seq.h:21, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:26: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CSeeker’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Seeker.cpp:1964:3: note: in expansion of macro ‘DeleteP’ 1964 | DeleteP(G->Seeker); | ^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveBond(PyMOLGlobals*, char const*, char const*, int, int, int, pymol::zstring_view)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:9484:67: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 200 and 210 [-Wformat-truncation=] 9484 | " Valence: %d bond valences adjusted in model \"%s\".\n", cnt, | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 314 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:9496:59: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 208 and 218 [-Wformat-truncation=] 9496 | " Unbond: %d bonds removed from model \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 41 and 306 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:9471:53: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 214 and 224 [-Wformat-truncation=] 9471 | " Bond: %d bonds added to model \"%s\".\n", cnt, rec->obj->Name | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 35 and 300 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 84%] Building CXX object CMakeFiles/_cmd.dir/layer3/Selector.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/Selector.cpp.o -MF CMakeFiles/_cmd.dir/layer3/Selector.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/Selector.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSetting(PyMOLGlobals*, int, _object*, pymol::zstring_view, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12004:70: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 217 [-Wformat-truncation=] 12004 | " Setting: %s set for %d atoms in object \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 42 or more bytes (assuming 297) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11915:42: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 237 [-Wformat-truncation=] 11915 | " Setting: %s set to %s in %d objects, state %d.\n", | ^~ 11916 | name, value, nObj, state + 1 ENDF(G); | ~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11915:21: note: directive argument in the range [1, 2147483647] 11915 | " Setting: %s set to %s in %d objects, state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11915:21: note: directive argument in the range [1, 2147483647] /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 43 or more bytes (assuming 1084) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11912:42: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 237 [-Wformat-truncation=] 11912 | " Setting: %s set to %s in %d objects.\n", name, value, nObj ENDF(G); | ^~ ~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11912:21: note: directive argument in the range [1, 2147483647] 11912 | " Setting: %s set to %s in %d objects.\n", name, value, nObj ENDF(G); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 34 or more bytes (assuming 1066) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12036:46: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 237 [-Wformat-truncation=] 12036 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~ 12037 | name, value, rec->obj->Name, state + 1 ENDF(G); | ~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12036:25: note: directive argument in the range [1, 2147483647] 12036 | " Setting: %s set to %s in object \"%s\", state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 43 or more bytes (assuming 1330) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12029:46: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 237 [-Wformat-truncation=] 12029 | " Setting: %s set to %s in object \"%s\".\n", | ^~ 12030 | name, value, rec->obj->Name ENDF(G); | ~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 34 or more bytes (assuming 1312) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:11871:39: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 237 [-Wformat-truncation=] 11871 | PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); | ^~ ~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 21 or more bytes (assuming 1044) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveUnsetSetting(PyMOLGlobals*, int, pymol::zstring_view, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12465:68: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 215 [-Wformat-truncation=] 12465 | " Setting: %s unset for %d atoms in object \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 44 or more bytes (assuming 299) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12487:57: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] 12487 | " Setting: %s unset in object \"%s\", state %d.\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12487:25: note: directive argument in the range [1, 2147483647] 12487 | " Setting: %s unset in object \"%s\", state %d.\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 41 or more bytes (assuming 305) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:12481:57: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] 12481 | " Setting: %s unset in object \"%s\".\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘snprintf’ output 32 or more bytes (assuming 287) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:41: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In member function ‘virtual bool SelectorAtomIterator::next()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:180:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 180 | if ((++a) >= selector->Table.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘bool SelectorIsSelectionDiscrete(PyMOLGlobals*, SelectorID_t, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1023:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1023 | for(int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorClassifyAtoms(PyMOLGlobals*, int, int, ObjectMolecule*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1077:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1077 | while(a < I->Table.size()) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1101:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1101 | while(a1 < I->Table.size()) { | ~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘const char* SelectorGetNameFromIndex(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1514:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1514 | for(int a = 1; a < I->Info.size(); a++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1648:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1648 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1675:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1675 | while(a1 < I->Table.size()) { | ~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1869:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1869 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorColorectionGet(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2682:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2682 | for(b = 0; b < n_used; b++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2698:16: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2698 | for(a = 0; a < n_used; a++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2710:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2710 | for(b = 0; b < n_used; b++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorColorectionApply(PyMOLGlobals*, PyObject*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2758:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 2758 | for(b = 0; b < n_used; b++) { /* update selection indices */ | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2763:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2763 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2767:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] 2767 | for(b = 0; b < n_used; b++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorSecretsAsPyList(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2868:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2868 | for(int a = 0; a < I->Info.size(); a++) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorAsPyList(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:2947:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2947 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCountStates(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3441:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3441 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCheckIntersection(PyMOLGlobals*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3465:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3465 | for(int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCountAtoms(PyMOLGlobals*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3483:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3483 | for(int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘void SelectorSetDeleteFlagOnSelectionInObject(PyMOLGlobals*, int, ObjectMolecule*, signed char)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3498:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3498 | for(int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int* SelectorGetIndexVLAImpl(PyMOLGlobals*, CSelector*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3584:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3584 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘void SelectorLogSele(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3643:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3643 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetSingleObjectMolecule(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3808:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3808 | for (a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetFirstObjectMolecule(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3838:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3838 | for (a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule** SelectorGetObjectMoleculeVLA(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:3862:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3862 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorSubdivide(PyMOLGlobals*, const char*, SelectorID_t, SelectorID_t, SelectorID_t, SelectorID_t, const char*, const char*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:4261:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4261 | for(a = 0; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorGetSeleNCSet(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:4565:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4565 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorGetArrayNCSet(PyMOLGlobals*, const sele_array_t&, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:4595:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4595 | for(a = start; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorMapMaskVDW(PyMOLGlobals*, int, ObjectMapState*, float, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:4749:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4749 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorMapGaussian(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, int, float)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:5109:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5109 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:5153:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5153 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorMapCoulomb(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, float)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:5361:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5361 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCreateObjectMolecule(PyMOLGlobals*, SelectorID_t, const char*, int, int, int, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6050:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 6050 | if(ob) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6054:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 6054 | SelectorUpdateTable(G, source, -1); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6065:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6065 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In lambda function: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6091:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6091 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6121:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6121 | for(a = cNDummyModels; a < I->Obj.size(); a++) { /* find bonds wholly contained in the selection */ | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6147:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6147 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6188:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6188 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6212:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6212 | for(a = cNDummyAtoms; a < I->Table.size(); a++) /* any selected atoms in this state? */ | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorEmbedSelection(PyMOLGlobals*, const int*, pymol::zstring_view, ObjectMolecule*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6648:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6648 | for(a = start; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘sele_array_t SelectorSelectFromTagDict(PyMOLGlobals*, const std::unordered_map&)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:6743:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6743 | for(int a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorModulate1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7281:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7281 | for (a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7304:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7304 | for(a = 0; ok && a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7367:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7367 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7381:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7381 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7404:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7404 | for(a = 0; ok && a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7445:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7445 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorSelect0(PyMOLGlobals*, EvalElem*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7478:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7478 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7489:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7489 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7494:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7494 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7501:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7501 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7505:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7505 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7509:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7509 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7513:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7513 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7517:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7517 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7526:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7526 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7543:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7543 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7548:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7548 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7553:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7553 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7558:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7558 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7563:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7563 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7568:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7568 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7573:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7573 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7577:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7577 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7581:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7581 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7586:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7586 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7591:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7591 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7598:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7598 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7614:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7614 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7620:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7620 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7629:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7629 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7641:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7641 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:7661:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7661 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘pymol::Result<> SelectorSelect1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8366:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8366 | for(a = cNDummyModels; a < I->Obj.size(); a++) | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8376:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8376 | else if(model > I->Obj.size()) | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorSelect2(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8458:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8458 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8462:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8462 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ [ 84%] Building CXX object CMakeFiles/_cmd.dir/layer3/SelectorTmp.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/SelectorTmp.cpp.o -MF CMakeFiles/_cmd.dir/layer3/SelectorTmp.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/SelectorTmp.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/SelectorTmp.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8510:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8510 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8521:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8521 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8532:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8532 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8543:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8543 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8558:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8558 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8569:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8569 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8580:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8580 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8591:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8591 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8606:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8606 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8617:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8617 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8628:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8628 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:8639:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8639 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorLogic1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9116:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9116 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9145:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9145 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorOperator22(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9404:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 9404 | for(a = 0; a < table_size; a++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9426:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9426 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9456:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9456 | for(a = 0; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9461:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9461 | for(a = cNDummyAtoms; a < I->Table.size(); a++) | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘pymol::Result > > SelectorEvaluate(PyMOLGlobals*, std::vector >&, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:9610:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9610 | while(ok && c < word.size()) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, float, float*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:10201:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10201 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, float*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:10483:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10483 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:10507:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10507 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, int, int, float*, int*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:10712:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10712 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:10789:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10789 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ [ 85%] Building CXX object CMakeFiles/_cmd.dir/layer3/SpecRec.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/SpecRec.cpp.o -MF CMakeFiles/_cmd.dir/layer3/SpecRec.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/SpecRec.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/SpecRec.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘CExecutive::drag(int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15625:55: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 15625 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", | ^~ 15626 | order_input, (location == -2) ? "upper" : "current"); | ~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:15625:26: note: ‘sprintf’ output between 32 and 1057 bytes into a destination of size 1024 15625 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 15626 | order_input, (location == -2) ? "upper" : "current"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object CMakeFiles/_cmd.dir/layer3/SpecRecSpecial.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/SpecRecSpecial.cpp.o -MF CMakeFiles/_cmd.dir/layer3/SpecRecSpecial.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/SpecRecSpecial.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/SpecRecSpecial.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveManageObject(PyMOLGlobals*, pymol::CObject*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14601:37: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] 14601 | " Executive-Warning: name \"%s\" collides with a selection language keyword.\n", | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 73 and 328 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14596:36: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] 14596 | " Executive: object name \"%s\" is illegal -- renamed to 'all_'.\n", obj->Name | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 61 and 316 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14627:11: warning: ‘strcpy’ offset 0 is out of the bounds [0, 0] [-Warray-bounds=] 14627 | strcpy(rec->name, obj->Name); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object CMakeFiles/_cmd.dir/layer4/Cmd.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer4/Cmd.cpp.o -MF CMakeFiles/_cmd.dir/layer4/Cmd.cpp.o.d -o CMakeFiles/_cmd.dir/layer4/Cmd.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp [ 86%] Building CXX object CMakeFiles/_cmd.dir/layer4/Menu.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer4/Menu.cpp.o -MF CMakeFiles/_cmd.dir/layer4/Menu.cpp.o.d -o CMakeFiles/_cmd.dir/layer4/Menu.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Menu.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveGroup(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:2275:40: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] 2275 | " Executive: adding '%s' to group '%s'.\n", rec.name, rec.group_name | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 36 and 546 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetName(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, bool)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:3535:41: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 222 [-Wformat-truncation=] 3535 | " Warning: Invalid characters in '%s' have been replaced or stripped\n", | ^~ 3536 | name ENDFB(G); | ~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 67 and 322 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5097:57: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 213 [-Wformat-truncation=] 5097 | " Executive: skipping unrecognized object \"%s\" of type %d.\n", | ^~ In function ‘ExecutiveSetNamedEntries(PyMOLGlobals*, _object*, int, int, int)’, inlined from ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5727:38: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 321 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5122:58: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 210 [-Wformat-truncation=] 5122 | "ExectiveSetNamedEntries-Error: after object \"%s\".\n", rec->name ENDFB(G); | ^~ In function ‘ExecutiveSetNamedEntries(PyMOLGlobals*, _object*, int, int, int)’, inlined from ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:5727:38: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 304 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:56: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 86%] Building CXX object CMakeFiles/_cmd.dir/layer4/PopUp.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer4/PopUp.cpp.o -MF CMakeFiles/_cmd.dir/layer4/PopUp.cpp.o.d -o CMakeFiles/_cmd.dir/layer4/PopUp.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/PopUp.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp: In function ‘PyObject* CmdPushUndo(PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:2199:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2199 | if(ok) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:2201:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2201 | if(s0[0]) | ^~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp: In function ‘PyObject* CmdGetMinMax(PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:4452:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 4452 | int ok = false; | ^~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:65: /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.h: In instantiation of ‘PyObject* PConvToPyObject(const std::array<_Tp, _Nm>&) [with T = float; long unsigned int N = 3; PyObject = _object]’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:365:27: required from ‘PyObject* APIResult(PyMOLGlobals*, pymol::Result&) [with T = std::array; PyObject = _object]’ 365 | return PConvToPyObject(res.result()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/Cmd.cpp:4017:19: required from here 4017 | return APIResult(G, result); | ~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PConv.h:259:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 259 | for (int i = 0; i < N; ++i) { | ~~^~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:24, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/P.h:22, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/PopUp.cpp:31: /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CPopUp’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer4/PopUp.cpp:402:3: note: in expansion of macro ‘DeleteP’ 402 | DeleteP(I); | ^~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1717:70: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] 1717 | " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", | ^~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:20: In function ‘snprintf’, inlined from ‘SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Selector.cpp:1716:19: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 59 and 324 bytes into a destination of size 255 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object CMakeFiles/_cmd.dir/layer5/PyMOL.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer5/PyMOL.cpp.o -MF CMakeFiles/_cmd.dir/layer5/PyMOL.cpp.o.d -o CMakeFiles/_cmd.dir/layer5/PyMOL.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp:35: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp: In function ‘PyMOLreturn_status Loader(CPyMOL*, const char*, const char*, int, const char*, const char*, int, int, int, int, int, int)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp:1586:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] 1586 | if((stop - start) >= sizeof(WordType)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp:23: /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp: In function ‘void PyMOL_Stop(CPyMOL*)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CMovie’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/PyMOL.cpp:2031:3: note: in expansion of macro ‘DeleteP’ 2031 | DeleteP(G->Movie); | ^~~~~~~ [ 87%] Building CXX object CMakeFiles/_cmd.dir/layer5/TestPyMOL.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer5/TestPyMOL.cpp.o -MF CMakeFiles/_cmd.dir/layer5/TestPyMOL.cpp.o.d -o CMakeFiles/_cmd.dir/layer5/TestPyMOL.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/TestPyMOL.cpp [ 87%] Building CXX object CMakeFiles/_cmd.dir/layer5/main.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer5/main.cpp.o -MF CMakeFiles/_cmd.dir/layer5/main.cpp.o.d -o CMakeFiles/_cmd.dir/layer5/main.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/main.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/TestPyMOL.cpp:35: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer5/main.cpp:53: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 88%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test.cpp [ 88%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Algorithm.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Algorithm.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Algorithm.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Algorithm.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Algorithm.cpp [ 88%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Bezier.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Bezier.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Bezier.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Bezier.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Bezier.cpp [ 89%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_CCrystal.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_CCrystal.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_CCrystal.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_CCrystal.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_CCrystal.cpp [ 89%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_CifFile.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_CifFile.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_CifFile.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_CifFile.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_CifFile.cpp [ 90%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Classic_VLA.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Classic_VLA.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Classic_VLA.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Classic_VLA.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Classic_VLA.cpp [ 90%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Event.cpp [ 90%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Executive.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Executive.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Executive.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Executive.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Executive.cpp [ 91%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Image.cpp In file included from /builddir/build/BUILD/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Executive.cpp:3: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 91%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_List.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_List.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_List.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_List.cpp.o -c /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_List.cpp /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Image.cpp: In function ‘void C_A_T_C_H_T_E_S_T_32()’: /builddir/build/BUILD/pymol-open-source-3.1.0/layerCTest/Test_Image.cpp:187:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 187 | for (int i = 0; i < img.getSizeInBytes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Picking.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-open-source-3.1.0/layer4 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CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_TTT.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_Test.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_Util.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_VLA.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_cache_ptr.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_copyable_ptr.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_type_traits.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_zstring_view.cpp.o CMakeFiles/_cmd.dir/ov/src/OVContext.cpp.o CMakeFiles/_cmd.dir/ov/src/OVHeap.cpp.o CMakeFiles/_cmd.dir/ov/src/OVHeapArray.cpp.o CMakeFiles/_cmd.dir/ov/src/OVLexicon.cpp.o CMakeFiles/_cmd.dir/ov/src/OVOneToAny.cpp.o CMakeFiles/_cmd.dir/ov/src/OVOneToOne.cpp.o CMakeFiles/_cmd.dir/ov/src/OVRandom.cpp.o CMakeFiles/_cmd.dir/ov/src/ov_utility.cpp.o -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -fopenmp /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘recreate_command_line’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1334:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1334 | line[0] = '\0'; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1333:26: note: destination object of size 0 allocated by ‘malloc’ 1333 | line = (char *) malloc (sizeof(char) * len); | ^ In member function ‘set_’, inlined from ‘__ct ’ at /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:119:6, inlined from ‘findBest’ at /builddir/build/BUILD/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:506:28: /builddir/build/BUILD/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:283:20: warning: ‘__builtin_memset’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 283 | *p = a; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveManageObject’: /builddir/build/BUILD/pymol-open-source-3.1.0/layer3/Executive.cpp:14627:11: warning: ‘strcpy’ writing between 1 and 256 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 14627 | strcpy(rec->name, obj->Name); | ^ lto1: note: destination object is likely at address zero In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1497:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1497:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1497:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [8, 12] into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 8 into destination object ‘nx’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [8, 12] into destination object ‘nx’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 8 into destination object ‘nx’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1498:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1498:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1498:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [8, 12] into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 8 into destination object ‘ny’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [8, 12] into destination object ‘ny’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 8 into destination object ‘ny’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1499:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1499:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:0, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_posn_momentum_v1’ at /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1499:24: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54: warning: writing 4 bytes into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [8, 12] into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 8 into destination object ‘nz’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [8, 12] into destination object ‘nz’ of size 4 /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 8 into destination object ‘nz’ of size 4 gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' [100%] Built target _cmd gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd/CMakeFiles 0 cmake /builddir/build/BUILD/pymol-open-source-3.1.0 -DTARGET_NAME=_champ -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/chempy/champ -DCMAKE_BUILD_TYPE=Release 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Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ cmake --build . --config Release -j4 /usr/bin/cmake -S/builddir/build/BUILD/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ/CMakeFiles /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' /usr/bin/gmake -f CMakeFiles/_champ.dir/build.make CMakeFiles/_champ.dir/depend gmake[2]: Entering directory 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function ‘OSMemoryZero’: /builddir/build/BUILD/pymol-open-source-3.1.0/contrib/champ/os_memory.c:55:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 55 | while(count&&(((int)p)&mask)) { | ^ [ 81%] Building C object CMakeFiles/_champ.dir/contrib/champ/strblock.c.o /usr/bin/gcc -D_champ_EXPORTS -I/builddir/build/BUILD/pymol-open-source-3.1.0/contrib/champ -I/usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/strblock.c.o -MF CMakeFiles/_champ.dir/contrib/champ/strblock.c.o.d -o 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/builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/chempy/champ/_champ.cpython-312-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/_champ.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,_champ.cpython-312-x86_64-linux-gnu.so -o /builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/chempy/champ/_champ.cpython-312-x86_64-linux-gnu.so CMakeFiles/_champ.dir/contrib/champ/champ.c.o CMakeFiles/_champ.dir/contrib/champ/champ_module.c.o CMakeFiles/_champ.dir/contrib/champ/chiral.c.o CMakeFiles/_champ.dir/contrib/champ/err2.c.o CMakeFiles/_champ.dir/contrib/champ/feedback2.c.o CMakeFiles/_champ.dir/contrib/champ/list.c.o CMakeFiles/_champ.dir/contrib/champ/os_memory.c.o CMakeFiles/_champ.dir/contrib/champ/sort.c.o CMakeFiles/_champ.dir/contrib/champ/strblock.c.o CMakeFiles/_champ.dir/contrib/champ/vla.c.o gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' [100%] Built target _champ gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ/CMakeFiles 0 running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-312/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-x86_64-cpython-312/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol2 copying modules/pymol/xwin.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/shortcut_manager.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/shortcut_dict.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/seqalign.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/save_shortcut.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/mpeg_encode.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/morphing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/lazyio.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/cgobuilder.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/_gui.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/__main__.py -> build/lib.linux-x86_64-cpython-312/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol creating build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-cpython-312/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-cpython-312/pmg_tk creating build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/shortcut_menu_gui.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/scene_bin_gui.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-x86_64-cpython-312/pmg_qt copying modules/chempy/xyz.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-cpython-312/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy creating build/lib.linux-x86_64-cpython-312/pymol_web creating build/lib.linux-x86_64-cpython-312/pymol_web/examples copying modules/pymol_web/examples/justhttpd.py -> build/lib.linux-x86_64-cpython-312/pymol_web/examples copying modules/pymol_web/examples/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol_web/examples creating build/lib.linux-x86_64-cpython-312/web creating build/lib.linux-x86_64-cpython-312/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-x86_64-cpython-312/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-x86_64-cpython-312/web/examples creating build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol/wizard creating build/lib.linux-x86_64-cpython-312/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol/stereochemistry creating build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol/plugins creating build/lib.linux-x86_64-cpython-312/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-x86_64-cpython-312/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-x86_64-cpython-312/pymol/Qt creating build/lib.linux-x86_64-cpython-312/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/startup creating build/lib.linux-x86_64-cpython-312/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/skins creating build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal creating build/lib.linux-x86_64-cpython-312/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_tk/skins/demo creating build/lib.linux-x86_64-cpython-312/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-x86_64-cpython-312/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-x86_64-cpython-312/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-x86_64-cpython-312/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_qt/syntax creating build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms creating build/lib.linux-x86_64-cpython-312/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-cpython-312/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-cpython-312/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-cpython-312/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-cpython-312/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/tinker creating build/lib.linux-x86_64-cpython-312/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-x86_64-cpython-312/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/mmtf creating build/lib.linux-x86_64-cpython-312/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/fragments creating build/lib.linux-x86_64-cpython-312/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/fast copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-cpython-312/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-cpython-312/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-cpython-312/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/champ creating build/lib.linux-x86_64-cpython-312/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-cpython-312/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-cpython-312/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-cpython-312/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-cpython-312/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-cpython-312/chempy/bmin running egg_info creating modules/pymol.egg-info writing modules/pymol.egg-info/PKG-INFO /usr/lib/python3.12/site-packages/setuptools/_core_metadata.py:157: SetuptoolsDeprecationWarning: Invalid config. !! ******************************************************************************** newlines are not allowed in `summary` and will break in the future ******************************************************************************** !! write_field('Summary', single_line(summary)) writing dependency_links to modules/pymol.egg-info/dependency_links.txt writing entry points to modules/pymol.egg-info/entry_points.txt writing requirements to modules/pymol.egg-info/requires.txt writing top-level names to modules/pymol.egg-info/top_level.txt writing manifest file 'modules/pymol.egg-info/SOURCES.txt' reading manifest file 'modules/pymol.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'modules/pymol.egg-info/SOURCES.txt' copying modules/pmg_qt/forms/shortcut_menu.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/help_shortcut.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/create_shortcut.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/change_confirm.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> build/lib.linux-x86_64-cpython-312/pmg_qt/forms running build_ext cmake /builddir/build/BUILD/pymol-open-source-3.1.0 -DTARGET_NAME=_cmd -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/pymol -DCMAKE_BUILD_TYPE=Release -DALL_INC_DIR=include;contrib/uiuc/plugins/include;ov/src;layer0;layer1;layer2;layer3;layer4;layer5;build/generated;contrib/uiuc/plugins/molfile_plugin/src;contrib/mmtf-c;layerCTest;/usr/lib64/python3.12/site-packages/numpy/core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.12;/usr/include/python3.12; -DALL_SRC=build/generated/ShaderText.cpp;contrib/mmtf-c/mmtf_parser.cpp;contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c;contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c;contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c;contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c;contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/carplugin.c;contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/corplugin.c;contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c;contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c;contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c;contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c;contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/hash.c;contrib/uiuc/plugins/molfile_plugin/src/inthash.c;contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c;contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c;contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c;contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c;contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c;contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c;contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c;contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c;contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c;contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c;contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp;contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c;layer0/Bezier.cpp;layer0/Block.cpp;layer0/CarveHelper.cpp;layer0/ContourSurf.cpp;layer0/Crystal.cpp;layer0/Err.cpp;layer0/Feedback.cpp;layer0/Field.cpp;layer0/File.cpp;layer0/GFXManager.cpp;layer0/GenericBuffer.cpp;layer0/GraphicsUtil.cpp;layer0/Isosurf.cpp;layer0/Map.cpp;layer0/Match.cpp;layer0/Matrix.cpp;layer0/MemoryDebug.cpp;layer0/MemoryUsage.cpp;layer0/MyPNG.cpp;layer0/Parse.cpp;layer0/Pixmap.cpp;layer0/PostProcess.cpp;layer0/PrintUtils.cpp;layer0/ShaderMgr.cpp;layer0/ShaderPreprocessor.cpp;layer0/ShaderPrg.cpp;layer0/Sphere.cpp;layer0/TTT.cpp;layer0/Tetsurf.cpp;layer0/Texture.cpp;layer0/Tracker.cpp;layer0/Triangle.cpp;layer0/Util.cpp;layer0/Util2.cpp;layer0/Vector.cpp;layer0/Word.cpp;layer0/ccealignmodule.cpp;layer0/marching_cubes.cpp;layer0/os_gl.cpp;layer1/Basis.cpp;layer1/ButMode.cpp;layer1/CGO.cpp;layer1/CGOGL.cpp;layer1/CGORenderer.cpp;layer1/COLLADA.cpp;layer1/Camera.cpp;layer1/Character.cpp;layer1/Color.cpp;layer1/Control.cpp;layer1/Extrude.cpp;layer1/Font.cpp;layer1/FontGLUT.cpp;layer1/FontGLUT8x13.cpp;layer1/FontGLUT9x15.cpp;layer1/FontGLUTHel10.cpp;layer1/FontGLUTHel12.cpp;layer1/FontGLUTHel18.cpp;layer1/FontType.cpp;layer1/ImageUtils.cpp;layer1/Movie.cpp;layer1/Ortho.cpp;layer1/P.cpp;layer1/PConv.cpp;layer1/Picking.cpp;layer1/Pop.cpp;layer1/PyMOLObject.cpp;layer1/Ray.cpp;layer1/Rep.cpp;layer1/Scene.cpp;layer1/SceneMouse.cpp;layer1/ScenePicking.cpp;layer1/SceneRay.cpp;layer1/SceneRender.cpp;layer1/SceneView.cpp;layer1/ScrollBar.cpp;layer1/Seq.cpp;layer1/Setting.cpp;layer1/Shaker.cpp;layer1/SymOp.cpp;layer1/SymOpPConv.cpp;layer1/SymOpTools.cpp;layer1/Symmetry.cpp;layer1/Text.cpp;layer1/TypeFace.cpp;layer1/View.cpp;layer1/Wizard.cpp;layer2/AssemblyHelpers.cpp;layer2/AtomInfo.cpp;layer2/AtomInfoHistory.cpp;layer2/BondTypeHistory.cpp;layer2/CifFile.cpp;layer2/CifMoleculeReader.cpp;layer2/CoordSet.cpp;layer2/DistSet.cpp;layer2/GadgetSet.cpp;layer2/HydrogenAdder.cpp;layer2/MmodTyping.cpp;layer2/MmtfMoleculeReader.cpp;layer2/Mol2Typing.cpp;layer2/MolV3000.cpp;layer2/ObjectAlignment.cpp;layer2/ObjectCGO.cpp;layer2/ObjectCallback.cpp;layer2/ObjectCurve.cpp;layer2/ObjectDist.cpp;layer2/ObjectGadget.cpp;layer2/ObjectGadgetRamp.cpp;layer2/ObjectGroup.cpp;layer2/ObjectMap.cpp;layer2/ObjectMesh.cpp;layer2/ObjectMolecule.cpp;layer2/ObjectMolecule2.cpp;layer2/ObjectMolecule3.cpp;layer2/ObjectSlice.cpp;layer2/ObjectSurface.cpp;layer2/ObjectVolume.cpp;layer2/RepAngle.cpp;layer2/RepCartoon.cpp;layer2/RepCylBond.cpp;layer2/RepDihedral.cpp;layer2/RepDistDash.cpp;layer2/RepDistLabel.cpp;layer2/RepDot.cpp;layer2/RepEllipsoid.cpp;layer2/RepLabel.cpp;layer2/RepMesh.cpp;layer2/RepNonbonded.cpp;layer2/RepNonbondedSphere.cpp;layer2/RepRibbon.cpp;layer2/RepSphere.cpp;layer2/RepSphereGenerate.cpp;layer2/RepSphereImmediate.cpp;layer2/RepSurface.cpp;layer2/RepWireBond.cpp;layer2/Sculpt.cpp;layer2/SculptCache.cpp;layer2/SideChainHelper.cpp;layer2/VFont.cpp;layer3/AtomIterators.cpp;layer3/CifDataValueFormatter.cpp;layer3/Editor.cpp;layer3/Executive.cpp;layer3/ExecutivePython.cpp;layer3/Interactions.cpp;layer3/MaeExportHelpers.cpp;layer3/MoleculeExporter.cpp;layer3/MovieScene.cpp;layer3/PlugIOManager.cpp;layer3/RingFinder.cpp;layer3/Seeker.cpp;layer3/Selector.cpp;layer3/SelectorTmp.cpp;layer3/SpecRec.cpp;layer3/SpecRecSpecial.cpp;layer4/Cmd.cpp;layer4/Menu.cpp;layer4/PopUp.cpp;layer5/PyMOL.cpp;layer5/TestPyMOL.cpp;layer5/main.cpp;layerCTest/Test.cpp;layerCTest/Test_Algorithm.cpp;layerCTest/Test_Bezier.cpp;layerCTest/Test_CCrystal.cpp;layerCTest/Test_CifFile.cpp;layerCTest/Test_Classic_VLA.cpp;layerCTest/Test_Event.cpp;layerCTest/Test_Executive.cpp;layerCTest/Test_Image.cpp;layerCTest/Test_List.cpp;layerCTest/Test_Picking.cpp;layerCTest/Test_Result.cpp;layerCTest/Test_ScrollBar.cpp;layerCTest/Test_ShaderPreprocessor.cpp;layerCTest/Test_SymOp.cpp;layerCTest/Test_TTT.cpp;layerCTest/Test_Test.cpp;layerCTest/Test_Util.cpp;layerCTest/Test_VLA.cpp;layerCTest/Test_cache_ptr.cpp;layerCTest/Test_copyable_ptr.cpp;layerCTest/Test_type_traits.cpp;layerCTest/Test_zstring_view.cpp;ov/src/OVContext.cpp;ov/src/OVHeap.cpp;ov/src/OVHeapArray.cpp;ov/src/OVLexicon.cpp;ov/src/OVOneToAny.cpp;ov/src/OVOneToOne.cpp;ov/src/OVRandom.cpp;ov/src/ov_utility.cpp; -DALL_DEF=_PYMOL_LIBPNG;_PYMOL_FREETYPE;PYMOL_OPENMP;_PYMOL_VMD_PLUGINS;_HAVE_LIBXML;MMTF_MSGPACK_USE_CPP11;MSGPACK_NO_BOOST;_PYMOL_NO_MAIN;_PYMOL_CTEST;_PYMOL_NUMPY; -DALL_LIB_DIR=/usr/lib64;/usr/lib; -DALL_LIB=png;freetype;xml2;GL;GLEW;netcdf; -DALL_COMP_ARGS=-Werror=return-type;-Wunused-variable;-Wno-switch;-Wno-narrowing;-Wno-char-subscripts;-O3;-fopenmp; -DALL_EXT_LINK=-fopenmp -DSHARED_SUFFIX=.cpython-312-x86_64-linux-gnu.so -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd cmake --build . --config Release -j4 /usr/bin/cmake -S/builddir/build/BUILD/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd/CMakeFiles /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' cd /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd/CMakeFiles/_cmd.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' gmake[2]: Nothing to be done for 'CMakeFiles/_cmd.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' [100%] Built target _cmd gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_cmd/CMakeFiles 0 cmake /builddir/build/BUILD/pymol-open-source-3.1.0 -DTARGET_NAME=_champ -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-312/chempy/champ -DCMAKE_BUILD_TYPE=Release -DALL_INC_DIR=contrib/champ;/usr/include/python3.12;/usr/include/python3.12; -DALL_SRC=contrib/champ/champ.c;contrib/champ/champ_module.c;contrib/champ/chiral.c;contrib/champ/err2.c;contrib/champ/feedback2.c;contrib/champ/list.c;contrib/champ/os_memory.c;contrib/champ/sort.c;contrib/champ/strblock.c;contrib/champ/vla.c; -DALL_DEF= -DALL_LIB_DIR=/usr/lib64;/usr/lib; -DALL_LIB= -DALL_COMP_ARGS= -DALL_EXT_LINK= -DSHARED_SUFFIX=.cpython-312-x86_64-linux-gnu.so -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ cmake --build . --config Release -j4 /usr/bin/cmake -S/builddir/build/BUILD/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ/CMakeFiles /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' /usr/bin/gmake -f CMakeFiles/_champ.dir/build.make CMakeFiles/_champ.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' cd /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ/CMakeFiles/_champ.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' /usr/bin/gmake -f CMakeFiles/_champ.dir/build.make CMakeFiles/_champ.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' gmake[2]: Nothing to be done for 'CMakeFiles/_champ.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' [100%] Built target _champ gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-312/_champ/CMakeFiles 0 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/web creating build/bdist.linux-x86_64/wheel/web/examples copying build/lib.linux-x86_64-cpython-312/web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/web/examples copying build/lib.linux-x86_64-cpython-312/web/examples/justhttpd.py -> build/bdist.linux-x86_64/wheel/web/examples creating build/bdist.linux-x86_64/wheel/pymol_web creating build/bdist.linux-x86_64/wheel/pymol_web/examples copying build/lib.linux-x86_64-cpython-312/pymol_web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/pymol_web/examples copying build/lib.linux-x86_64-cpython-312/pymol_web/examples/justhttpd.py -> build/bdist.linux-x86_64/wheel/pymol_web/examples creating build/bdist.linux-x86_64/wheel/pmg_qt creating build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/askpartial.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/change_confirm.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/colors.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/create_shortcut.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/fetch.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/help_shortcut.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/load_aln.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/load_mae.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/load_map.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/load_mtz.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/load_traj.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/movieexport.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/pluginitem.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/pluginmanager.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/png.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/props.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/render.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/save_molecule.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/save_object.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/shortcut_menu.ui -> build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-312/pmg_qt/forms/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_qt/forms creating build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-312/pmg_qt/syntax/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-312/pmg_qt/syntax/pml.py -> build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-312/pmg_qt/syntax/pmlparser.py -> build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-312/pmg_qt/syntax/python.py -> build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-312/pmg_qt/TextEditor.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/advanced_settings_gui.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/builder.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/file_dialogs.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/keymapping.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/mimic_pmg_tk.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/mimic_tk.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/properties_dialog.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/pymol_gl_widget.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/pymol_qt_gui.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/scene_bin_gui.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/shortcut_menu_gui.py -> build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-312/pmg_qt/volume.py -> build/bdist.linux-x86_64/wheel/pmg_qt creating build/bdist.linux-x86_64/wheel/pmg_tk creating build/bdist.linux-x86_64/wheel/pmg_tk/skins creating build/bdist.linux-x86_64/wheel/pmg_tk/skins/demo copying build/lib.linux-x86_64-cpython-312/pmg_tk/skins/demo/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_tk/skins/demo creating build/bdist.linux-x86_64/wheel/pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal/ModalWindow.py -> build/bdist.linux-x86_64/wheel/pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-312/pmg_tk/skins/normal/builder.py -> build/bdist.linux-x86_64/wheel/pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-312/pmg_tk/skins/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_tk/skins creating build/bdist.linux-x86_64/wheel/pmg_tk/startup copying build/lib.linux-x86_64-cpython-312/pmg_tk/startup/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_tk/startup copying build/lib.linux-x86_64-cpython-312/pmg_tk/ColorEditor.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/Demo.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/PyMOLMapLoad.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/SetEditor.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/Setting.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/TextEditor.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/__init__.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/volume.py -> build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-312/pmg_tk/PMGApp.py -> build/bdist.linux-x86_64/wheel/pmg_tk creating build/bdist.linux-x86_64/wheel/pymol2 copying build/lib.linux-x86_64-cpython-312/pymol2/__init__.py -> build/bdist.linux-x86_64/wheel/pymol2 copying build/lib.linux-x86_64-cpython-312/pymol2/cmd2.py -> build/bdist.linux-x86_64/wheel/pymol2 creating build/bdist.linux-x86_64/wheel/chempy creating build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-312/chempy/bmin/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-312/chempy/bmin/commands.py -> build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-312/chempy/bmin/realtime.py -> build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-312/chempy/bmin/state.py -> build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-312/chempy/bmin/util.py -> build/bdist.linux-x86_64/wheel/chempy/bmin creating build/bdist.linux-x86_64/wheel/chempy/fast copying build/lib.linux-x86_64-cpython-312/chempy/fast/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/fast creating build/bdist.linux-x86_64/wheel/chempy/fragments copying build/lib.linux-x86_64-cpython-312/chempy/fragments/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/fragments creating build/bdist.linux-x86_64/wheel/chempy/mmtf copying build/lib.linux-x86_64-cpython-312/chempy/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/mmtf copying build/lib.linux-x86_64-cpython-312/chempy/mmtf/io.py -> build/bdist.linux-x86_64/wheel/chempy/mmtf creating build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/tinker/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/tinker/amber.py -> build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/tinker/keyword.py -> build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/tinker/realtime.py -> build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/tinker/state.py -> build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-312/chempy/__init__.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/arc.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/bond_amber.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/bond_mmff.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/bonds.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/brick.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/cc1.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/charge.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/cif.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/cpv.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/dictdb.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/gamess1.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/gms.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/hetatm.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/io.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/lst.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/mae.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/map.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/mass.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/mmd.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/models.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/mol.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/mol2.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/neighbor.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/pdb.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/pkl.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/place.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/protein.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/protein_amber.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/protein_amber99.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/protein_mmff.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/protein_residues.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/sdf.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/solvate.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/water_amber.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/water_residues.py -> build/bdist.linux-x86_64/wheel/chempy copying build/lib.linux-x86_64-cpython-312/chempy/xyz.py -> build/bdist.linux-x86_64/wheel/chempy creating build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-312/chempy/champ/__init__.py -> build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-312/chempy/champ/amber99.py -> build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-312/chempy/champ/assign.py -> build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-312/chempy/champ/formal_charges.py -> build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-312/chempy/champ/_champ.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/chempy/champ creating build/bdist.linux-x86_64/wheel/pymol creating build/bdist.linux-x86_64/wheel/pymol/Qt copying build/lib.linux-x86_64-cpython-312/pymol/Qt/__init__.py -> build/bdist.linux-x86_64/wheel/pymol/Qt copying build/lib.linux-x86_64-cpython-312/pymol/Qt/utils.py -> build/bdist.linux-x86_64/wheel/pymol/Qt creating build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/__init__.py -> build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/installation.py -> build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/legacysupport.py -> build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/managergui.py -> build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/managergui_qt.py -> build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-312/pymol/plugins/repository.py -> build/bdist.linux-x86_64/wheel/pymol/plugins creating build/bdist.linux-x86_64/wheel/pymol/stereochemistry copying build/lib.linux-x86_64-cpython-312/pymol/stereochemistry/__init__.py -> build/bdist.linux-x86_64/wheel/pymol/stereochemistry creating build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/__init__.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/annotation.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/appearance.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/benchmark.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/box.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/charge.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/cleanup.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/command.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/demo.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/density.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/distance.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/dragging.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/filter.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/label.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/measurement.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/message.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/mutagenesis.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/nucmutagenesis.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/openvr.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/pair_fit.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/pseudoatom.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/renaming.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/sculpting.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/security.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/stereodemo.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/wizard/toggle.py -> build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-312/pymol/__init__.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/__main__.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/_gui.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/api.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/callback.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/cgo.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/cgobuilder.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/checking.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/cmd.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/colorprinting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/colorramping.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/commanding.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/completing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/computing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/constants.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/constants_palette.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/controlling.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/creating.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/diagnosing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/editing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/editor.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/experimenting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/exporting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/externing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/feedingback.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/fitting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/gui.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/headering.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/helping.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/importing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/internal.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/invocation.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/keyboard.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/keywords.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/lazyio.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/locking.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/menu.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/monitoring.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/morphing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/movie.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/moving.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/mpeg_encode.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/parser.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/parsing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/povray.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/preset.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/pymolhttpd.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/querying.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/rpc.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/save_shortcut.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/selecting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/selector.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/seqalign.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/setting.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/shortcut.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/shortcut_dict.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/shortcut_manager.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/util.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/vfont.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/viewing.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/wizarding.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/xray.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/xwin.py -> build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-312/pymol/_cmd.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/pymol running install_egg_info Copying modules/pymol.egg-info to build/bdist.linux-x86_64/wheel/pymol-3.1.0-py3.12.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pymol/pymol_path copying LICENSE -> build/bdist.linux-x86_64/wheel/pymol/pymol_path copying data -> build/bdist.linux-x86_64/wheel/pymol/pymol_path/data copying test -> build/bdist.linux-x86_64/wheel/pymol/pymol_path/test copying examples -> build/bdist.linux-x86_64/wheel/pymol/pymol_path/examples creating build/bdist.linux-x86_64/wheel/pymol-3.1.0.data creating build/bdist.linux-x86_64/wheel/pymol-3.1.0.data/scripts creating build/bdist.linux-x86_64/wheel/pymol-3.1.0.dist-info/WHEEL creating '/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir/pip-modern-metadata-9kc_6gqi/.tmp-1d49jlh7/pymol-3.1.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'chempy/__init__.py' adding 'chempy/arc.py' adding 'chempy/bond_amber.py' adding 'chempy/bond_mmff.py' adding 'chempy/bonds.py' adding 'chempy/brick.py' adding 'chempy/cc1.py' adding 'chempy/charge.py' adding 'chempy/cif.py' adding 'chempy/cpv.py' adding 'chempy/dictdb.py' adding 'chempy/gamess1.py' adding 'chempy/gms.py' adding 'chempy/hetatm.py' adding 'chempy/io.py' adding 'chempy/lst.py' adding 'chempy/mae.py' adding 'chempy/map.py' adding 'chempy/mass.py' adding 'chempy/mmd.py' adding 'chempy/models.py' adding 'chempy/mol.py' adding 'chempy/mol2.py' adding 'chempy/neighbor.py' adding 'chempy/pdb.py' adding 'chempy/pkl.py' adding 'chempy/place.py' adding 'chempy/protein.py' adding 'chempy/protein_amber.py' adding 'chempy/protein_amber99.py' adding 'chempy/protein_mmff.py' adding 'chempy/protein_residues.py' adding 'chempy/sdf.py' adding 'chempy/solvate.py' adding 'chempy/water_amber.py' adding 'chempy/water_residues.py' adding 'chempy/xyz.py' adding 'chempy/bmin/__init__.py' adding 'chempy/bmin/commands.py' adding 'chempy/bmin/realtime.py' adding 'chempy/bmin/state.py' adding 'chempy/bmin/util.py' adding 'chempy/champ/__init__.py' adding 'chempy/champ/_champ.cpython-312-x86_64-linux-gnu.so' adding 'chempy/champ/amber99.py' adding 'chempy/champ/assign.py' adding 'chempy/champ/formal_charges.py' adding 'chempy/fast/__init__.py' adding 'chempy/fragments/__init__.py' adding 'chempy/mmtf/__init__.py' adding 'chempy/mmtf/io.py' adding 'chempy/tinker/__init__.py' adding 'chempy/tinker/amber.py' adding 'chempy/tinker/keyword.py' adding 'chempy/tinker/realtime.py' adding 'chempy/tinker/state.py' adding 'pmg_qt/TextEditor.py' adding 'pmg_qt/__init__.py' adding 'pmg_qt/advanced_settings_gui.py' adding 'pmg_qt/builder.py' adding 'pmg_qt/file_dialogs.py' adding 'pmg_qt/keymapping.py' adding 'pmg_qt/mimic_pmg_tk.py' adding 'pmg_qt/mimic_tk.py' adding 'pmg_qt/properties_dialog.py' adding 'pmg_qt/pymol_gl_widget.py' adding 'pmg_qt/pymol_qt_gui.py' adding 'pmg_qt/scene_bin_gui.py' adding 'pmg_qt/shortcut_menu_gui.py' adding 'pmg_qt/volume.py' adding 'pmg_qt/forms/__init__.py' adding 'pmg_qt/forms/askpartial.ui' adding 'pmg_qt/forms/change_confirm.ui' adding 'pmg_qt/forms/colors.ui' adding 'pmg_qt/forms/create_shortcut.ui' adding 'pmg_qt/forms/fetch.ui' adding 'pmg_qt/forms/help_shortcut.ui' adding 'pmg_qt/forms/load_aln.ui' adding 'pmg_qt/forms/load_mae.ui' adding 'pmg_qt/forms/load_map.ui' adding 'pmg_qt/forms/load_mtz.ui' adding 'pmg_qt/forms/load_traj.ui' adding 'pmg_qt/forms/movieexport.ui' adding 'pmg_qt/forms/pluginitem.ui' adding 'pmg_qt/forms/pluginmanager.ui' adding 'pmg_qt/forms/png.ui' adding 'pmg_qt/forms/props.ui' adding 'pmg_qt/forms/render.ui' adding 'pmg_qt/forms/save_molecule.ui' adding 'pmg_qt/forms/save_object.ui' adding 'pmg_qt/forms/shortcut_menu.ui' adding 'pmg_qt/syntax/__init__.py' adding 'pmg_qt/syntax/pml.py' adding 'pmg_qt/syntax/pmlparser.py' adding 'pmg_qt/syntax/python.py' adding 'pmg_tk/ColorEditor.py' adding 'pmg_tk/Demo.py' adding 'pmg_tk/PMGApp.py' adding 'pmg_tk/PyMOLMapLoad.py' adding 'pmg_tk/SetEditor.py' adding 'pmg_tk/Setting.py' adding 'pmg_tk/TextEditor.py' adding 'pmg_tk/__init__.py' adding 'pmg_tk/volume.py' adding 'pmg_tk/skins/__init__.py' adding 'pmg_tk/skins/demo/__init__.py' adding 'pmg_tk/skins/normal/ModalWindow.py' adding 'pmg_tk/skins/normal/__init__.py' adding 'pmg_tk/skins/normal/builder.py' adding 'pmg_tk/startup/__init__.py' adding 'pymol/__init__.py' adding 'pymol/__main__.py' adding 'pymol/_cmd.cpython-312-x86_64-linux-gnu.so' adding 'pymol/_gui.py' adding 'pymol/api.py' adding 'pymol/callback.py' adding 'pymol/cgo.py' adding 'pymol/cgobuilder.py' adding 'pymol/checking.py' adding 'pymol/cmd.py' adding 'pymol/colorprinting.py' adding 'pymol/colorramping.py' adding 'pymol/commanding.py' adding 'pymol/completing.py' adding 'pymol/computing.py' adding 'pymol/constants.py' adding 'pymol/constants_palette.py' adding 'pymol/controlling.py' adding 'pymol/creating.py' adding 'pymol/diagnosing.py' adding 'pymol/editing.py' adding 'pymol/editor.py' adding 'pymol/experimenting.py' adding 'pymol/exporting.py' adding 'pymol/externing.py' adding 'pymol/feedingback.py' adding 'pymol/fitting.py' adding 'pymol/gui.py' adding 'pymol/headering.py' adding 'pymol/helping.py' adding 'pymol/importing.py' adding 'pymol/internal.py' adding 'pymol/invocation.py' adding 'pymol/keyboard.py' adding 'pymol/keywords.py' adding 'pymol/lazyio.py' adding 'pymol/locking.py' adding 'pymol/menu.py' adding 'pymol/monitoring.py' adding 'pymol/morphing.py' adding 'pymol/movie.py' adding 'pymol/moving.py' adding 'pymol/mpeg_encode.py' adding 'pymol/parser.py' adding 'pymol/parsing.py' adding 'pymol/povray.py' adding 'pymol/preset.py' adding 'pymol/pymolhttpd.py' adding 'pymol/querying.py' adding 'pymol/rpc.py' adding 'pymol/save_shortcut.py' adding 'pymol/selecting.py' adding 'pymol/selector.py' adding 'pymol/seqalign.py' adding 'pymol/setting.py' adding 'pymol/shortcut.py' adding 'pymol/shortcut_dict.py' adding 'pymol/shortcut_manager.py' adding 'pymol/util.py' adding 'pymol/vfont.py' adding 'pymol/viewing.py' adding 'pymol/wizarding.py' adding 'pymol/xray.py' adding 'pymol/xwin.py' adding 'pymol/Qt/__init__.py' adding 'pymol/Qt/utils.py' adding 'pymol/plugins/__init__.py' adding 'pymol/plugins/installation.py' adding 'pymol/plugins/legacysupport.py' adding 'pymol/plugins/managergui.py' adding 'pymol/plugins/managergui_qt.py' adding 'pymol/plugins/repository.py' adding 'pymol/pymol_path/LICENSE' adding 'pymol/pymol_path/data/chem_comp_bond-top100.cif' adding 'pymol/pymol_path/data/setting_help.csv' adding 'pymol/pymol_path/data/chempy/water.pdb' adding 'pymol/pymol_path/data/chempy/fragments/ace.pkl' adding 'pymol/pymol_path/data/chempy/fragments/acetylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/benzene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/butane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_val.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyanide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ethylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formamide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formic.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/indane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/methane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/methanol.pkl' adding 'pymol/pymol_path/data/chempy/fragments/napthylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nhh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nitro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nme.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_val.pkl' adding 'pymol/pymol_path/data/chempy/fragments/peptide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/phosphite.pkl' adding 'pymol/pymol_path/data/chempy/fragments/pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/realtime.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/sulfone.pkl' adding 'pymol/pymol_path/data/chempy/fragments/thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/utp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/utpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/val.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/generate1.py' adding 'pymol/pymol_path/data/chempy/sidechains/generate2.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_library.pkl' adding 'pymol/pymol_path/data/chempy/tinker/Makefile.delsci' adding 'pymol/pymol_path/data/chempy/tinker/chempy.prm' adding 'pymol/pymol_path/data/chempy/tinker/make99_simple.py' adding 'pymol/pymol_path/data/chempy/tinker/make_simple.py' adding 'pymol/pymol_path/data/chempy/tinker/parm94.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm96.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99_simple.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99_wld.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm_simple.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm_simple.inp' adding 'pymol/pymol_path/data/demo/1hpv.r3d' adding 'pymol/pymol_path/data/demo/1tii.pdb' adding 'pymol/pymol_path/data/demo/cgo03.py' adding 'pymol/pymol_path/data/demo/il2.pdb' adding 'pymol/pymol_path/data/demo/pept.pdb' adding 'pymol/pymol_path/data/demo/pept.pkl' adding 'pymol/pymol_path/data/openvr/actions.json' adding 'pymol/pymol_path/data/openvr/bindings_vive_controller.json' adding 'pymol/pymol_path/data/openvr/hints_vive_controller.png' adding 'pymol/pymol_path/data/openvr/hints_vive_controller.svg' adding 'pymol/pymol_path/data/openvr/menu_splash.png' adding 'pymol/pymol_path/data/openvr/menu_splash.svg' adding 'pymol/pymol_path/data/pmg_qt/icons/refresh.svg' adding 'pymol/pymol_path/data/pmg_qt/styles/pymol.sty' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm' adding 'pymol/pymol_path/data/pymol/cmyk.png' adding 'pymol/pymol_path/data/pymol/hsv.ppm' adding 'pymol/pymol_path/data/pymol/splash.png' adding 'pymol/pymol_path/data/pymol/icons/icon2.svg' adding 'pymol/pymol_path/data/pymol/matrices/BLOSUM62' adding 'pymol/pymol_path/data/shaders/anaglyph_header.fs' adding 'pymol/pymol_path/data/shaders/bezier.fs' adding 'pymol/pymol_path/data/shaders/bezier.tsc' adding 'pymol/pymol_path/data/shaders/bezier.tse' adding 'pymol/pymol_path/data/shaders/bezier.vs' adding 'pymol/pymol_path/data/shaders/bg.fs' adding 'pymol/pymol_path/data/shaders/bg.vs' adding 'pymol/pymol_path/data/shaders/call_compute_color_for_light.fs' adding 'pymol/pymol_path/data/shaders/compute_color_for_light.fs' adding 'pymol/pymol_path/data/shaders/compute_fog_color.fs' adding 'pymol/pymol_path/data/shaders/connector.fs' adding 'pymol/pymol_path/data/shaders/connector.gs' adding 'pymol/pymol_path/data/shaders/connector.shared' adding 'pymol/pymol_path/data/shaders/connector.vs' adding 'pymol/pymol_path/data/shaders/copy.fs' adding 'pymol/pymol_path/data/shaders/copy.vs' adding 'pymol/pymol_path/data/shaders/cylinder.fs' adding 'pymol/pymol_path/data/shaders/cylinder.vs' adding 'pymol/pymol_path/data/shaders/default.fs' adding 'pymol/pymol_path/data/shaders/default.vs' adding 'pymol/pymol_path/data/shaders/indicator.fs' adding 'pymol/pymol_path/data/shaders/indicator.vs' adding 'pymol/pymol_path/data/shaders/label.fs' adding 'pymol/pymol_path/data/shaders/label.vs' adding 'pymol/pymol_path/data/shaders/line.fs' adding 'pymol/pymol_path/data/shaders/line.vs' adding 'pymol/pymol_path/data/shaders/oit.fs' adding 'pymol/pymol_path/data/shaders/oit.vs' adding 'pymol/pymol_path/data/shaders/ramp.fs' adding 'pymol/pymol_path/data/shaders/ramp.vs' adding 'pymol/pymol_path/data/shaders/screen.fs' adding 'pymol/pymol_path/data/shaders/screen.vs' adding 'pymol/pymol_path/data/shaders/sphere.fs' adding 'pymol/pymol_path/data/shaders/sphere.vs' adding 'pymol/pymol_path/data/shaders/surface.fs' adding 'pymol/pymol_path/data/shaders/surface.vs' adding 'pymol/pymol_path/data/shaders/trilines.fs' adding 'pymol/pymol_path/data/shaders/trilines.vs' adding 'pymol/pymol_path/data/shaders/volume.fs' adding 'pymol/pymol_path/data/shaders/volume.vs' adding 'pymol/pymol_path/data/shaders/vrcontroller.fs' adding 'pymol/pymol_path/data/shaders/vrcontroller.vs' adding 'pymol/pymol_path/data/shaders/webgl_header.fs' adding 'pymol/pymol_path/data/shaders/webgl_header.vs' adding 'pymol/pymol_path/data/startup/README.txt' adding 'pymol/pymol_path/data/startup/apbs_gui/__init__.py' adding 'pymol/pymol_path/data/startup/apbs_gui/apbs.ui' adding 'pymol/pymol_path/data/startup/apbs_gui/creating.py' adding 'pymol/pymol_path/data/startup/apbs_gui/electrostatics.py' adding 'pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py' adding 'pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py' adding 'pymol/pymol_path/data/startup/lightingsettings_gui/main.py' adding 'pymol/pymol_path/data/test/double.png' adding 'pymol/pymol_path/data/test/single-right.png' adding 'pymol/pymol_path/data/test/single.png' adding 'pymol/pymol_path/data/tut/1hpv.pdb' adding 'pymol/pymol_path/examples/chempy/generate_amber.py' adding 'pymol/pymol_path/examples/chempy/generate_mmff.py' adding 'pymol/pymol_path/examples/cookbook/area_diff.pml' adding 'pymol/pymol_path/examples/cookbook/build_peptide.py' adding 'pymol/pymol_path/examples/cookbook/contact.pml' adding 'pymol/pymol_path/examples/cookbook/dali.py' adding 'pymol/pymol_path/examples/cookbook/density.pml' adding 'pymol/pymol_path/examples/cookbook/groel_es.pml' adding 'pymol/pymol_path/examples/cookbook/multiclip_ray.pml' adding 'pymol/pymol_path/examples/cookbook/packing.pml' adding 'pymol/pymol_path/examples/cookbook/packsurf.pml' adding 'pymol/pymol_path/examples/cookbook/ref_frame.pml' adding 'pymol/pymol_path/examples/cookbook/ribosome.pml' adding 'pymol/pymol_path/examples/cookbook/scenes2movie.pml' adding 'pymol/pymol_path/examples/cookbook/seq_match_sele.pml' adding 'pymol/pymol_path/examples/cookbook/ss_xfer.pml' adding 'pymol/pymol_path/examples/cookbook/symsph.py' adding 'pymol/pymol_path/examples/devel/brick01.py' adding 'pymol/pymol_path/examples/devel/cam2crd.pym' adding 'pymol/pymol_path/examples/devel/cgo01.py' adding 'pymol/pymol_path/examples/devel/cgo02.py' adding 'pymol/pymol_path/examples/devel/cgo03.py' adding 'pymol/pymol_path/examples/devel/cgo04.py' adding 'pymol/pymol_path/examples/devel/cgo05.py' adding 'pymol/pymol_path/examples/devel/cgo06.py' adding 'pymol/pymol_path/examples/devel/cgo07.py' adding 'pymol/pymol_path/examples/devel/cgo08.py' adding 'pymol/pymol_path/examples/devel/cgo_3Dtext01.py' adding 'pymol/pymol_path/examples/devel/cgo_axes.py' adding 'pymol/pymol_path/examples/devel/cgo_label_hack.py' adding 'pymol/pymol_path/examples/devel/cgo_plane.py' adding 'pymol/pymol_path/examples/devel/chempy_model01.py' adding 'pymol/pymol_path/examples/devel/chempy_model02.py' adding 'pymol/pymol_path/examples/devel/chempy_model03.py' adding 'pymol/pymol_path/examples/devel/click_ordered_list.py' adding 'pymol/pymol_path/examples/devel/count_molecules.py' adding 'pymol/pymol_path/examples/devel/demo.sdf' adding 'pymol/pymol_path/examples/devel/extend_demo01.py' adding 'pymol/pymol_path/examples/devel/gl01.py' adding 'pymol/pymol_path/examples/devel/gl02.py' adding 'pymol/pymol_path/examples/devel/gl03.py' adding 'pymol/pymol_path/examples/devel/hole_vmd_tri.pym' adding 'pymol/pymol_path/examples/devel/importing.py' adding 'pymol/pymol_path/examples/devel/link_demo.py' adding 'pymol/pymol_path/examples/devel/membrane.py' adding 'pymol/pymol_path/examples/devel/mutate01.pml' adding 'pymol/pymol_path/examples/devel/mutate02.py' adding 'pymol/pymol_path/examples/devel/my_ext_gui.py' adding 'pymol/pymol_path/examples/devel/particle01.py' adding 'pymol/pymol_path/examples/devel/particle02.py' adding 'pymol/pymol_path/examples/devel/pick_wiz.py' adding 'pymol/pymol_path/examples/devel/povray01.py' adding 'pymol/pymol_path/examples/devel/scenes_to_movie01.pml' adding 'pymol/pymol_path/examples/devel/sd_annotate.pml' adding 'pymol/pymol_path/examples/devel/sele_wiz.py' adding 'pymol/pymol_path/examples/devel/start_pymol.py' adding 'pymol/pymol_path/examples/devel/syncmol.py' adding 'pymol/pymol_path/examples/devel/tkwindow.py' adding 'pymol/pymol_path/examples/devel/webgui01.py' adding 'pymol/pymol_path/examples/devel/webgui02.py' adding 'pymol/pymol_path/examples/devel/xmlrpc01.py' adding 'pymol/pymol_path/examples/devel/xmlrpc02.py' adding 'pymol/pymol_path/examples/launching/README' adding 'pymol/pymol_path/examples/launching/launch_demo.py' adding 'pymol/pymol_path/examples/launching/launch_viewer1.py' adding 'pymol/pymol_path/examples/launching/launch_viewer2.py' adding 'pymol/pymol_path/test/dat/1tii.pdb' adding 'pymol/pymol_path/test/dat/3al1.pdb' adding 'pymol/pymol_path/test/dat/3al1.r3d' adding 'pymol/pymol_path/test/dat/embed01.p1m' adding 'pymol/pymol_path/test/dat/embed02.p1m' adding 'pymol/pymol_path/test/dat/embed03.p1m' adding 'pymol/pymol_path/test/dat/embed04.p1m' adding 'pymol/pymol_path/test/dat/embed05.p1m' adding 'pymol/pymol_path/test/dat/embed06.p1m' adding 'pymol/pymol_path/test/dat/helix_amber.pdb' adding 'pymol/pymol_path/test/dat/il2.pdb' adding 'pymol/pymol_path/test/dat/ligs3d.sdf' adding 'pymol/pymol_path/test/dat/names.pdb' adding 'pymol/pymol_path/test/dat/odd01.pdb' adding 'pymol/pymol_path/test/dat/odd02.pdb' adding 'pymol/pymol_path/test/dat/pept.pdb' adding 'pymol/pymol_path/test/dat/pept.pkl' adding 'pymol/pymol_path/test/dat/pept.r3d' adding 'pymol/pymol_path/test/dat/small01.mol' adding 'pymol/pymol_path/test/dat/small02.pdb' adding 'pymol/pymol_path/test/dat/small03.mol2' adding 'pymol/pymol_path/test/dat/tiny.pdb' adding 'pymol/pymol_path/test/dat/water.pdb' adding 'pymol/stereochemistry/__init__.py' adding 'pymol/wizard/__init__.py' adding 'pymol/wizard/annotation.py' adding 'pymol/wizard/appearance.py' adding 'pymol/wizard/benchmark.py' adding 'pymol/wizard/box.py' adding 'pymol/wizard/charge.py' adding 'pymol/wizard/cleanup.py' adding 'pymol/wizard/command.py' adding 'pymol/wizard/demo.py' adding 'pymol/wizard/density.py' adding 'pymol/wizard/distance.py' adding 'pymol/wizard/dragging.py' adding 'pymol/wizard/filter.py' adding 'pymol/wizard/label.py' adding 'pymol/wizard/measurement.py' adding 'pymol/wizard/message.py' adding 'pymol/wizard/mutagenesis.py' adding 'pymol/wizard/nucmutagenesis.py' adding 'pymol/wizard/openvr.py' adding 'pymol/wizard/pair_fit.py' adding 'pymol/wizard/pseudoatom.py' adding 'pymol/wizard/renaming.py' adding 'pymol/wizard/sculpting.py' adding 'pymol/wizard/security.py' adding 'pymol/wizard/stereodemo.py' adding 'pymol/wizard/toggle.py' adding 'pymol-3.1.0.data/scripts/pymol' adding 'pymol2/__init__.py' adding 'pymol2/cmd2.py' adding 'pymol_web/examples/__init__.py' adding 'pymol_web/examples/justhttpd.py' adding 'web/examples/__init__.py' adding 'web/examples/justhttpd.py' adding 'pymol-3.1.0.dist-info/AUTHORS' adding 'pymol-3.1.0.dist-info/LICENSE' adding 'pymol-3.1.0.dist-info/METADATA' adding 'pymol-3.1.0.dist-info/WHEEL' adding 'pymol-3.1.0.dist-info/entry_points.txt' adding 'pymol-3.1.0.dist-info/top_level.txt' adding 'pymol-3.1.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: pymol Building wheel for pymol (pyproject.toml): started Running command Building wheel for pymol (pyproject.toml) Building wheel for pymol (pyproject.toml): finished with status 'done' Created wheel for pymol: filename=pymol-3.1.0-cp312-cp312-linux_x86_64.whl size=44356014 sha256=fee9ea293f4bc5f3100163dd0be8e35ccda9faf14ccb9988fa5f5cd5c1ce6616 Stored in directory: /builddir/.cache/pip/wheels/98/63/f9/50f55feb2bd95abf7ab5e7cbf59a609ee5aa94c5fe50cd2fb9 Successfully built pymol + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.pyFcrA + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 ++ dirname /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 ++ ls /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir/pymol-3.1.0-cp312-cp312-linux_x86_64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=pymol==3.1.0 + '[' -z pymol==3.1.0 ']' + TMPDIR=/builddir/build/BUILD/pymol-open-source-3.1.0/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir pymol==3.1.0 Using pip 23.3.2 from /usr/lib/python3.12/site-packages/pip (python 3.12) Looking in links: /builddir/build/BUILD/pymol-open-source-3.1.0/pyproject-wheeldir Processing ./pyproject-wheeldir/pymol-3.1.0-cp312-cp312-linux_x86_64.whl Installing collected packages: pymol Creating /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin changing mode of /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin/pymol to 755 Successfully installed pymol-3.1.0 + '[' -d /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin ']' + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin/pymol /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin/pymol: updating + rm -rfv /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin/__pycache__ + rm -f /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib/python3.12/site-packages ']' + '[' /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages '!=' /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib/python3.12/site-packages ']' + '[' -d /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages ']' + site_dirs+=("/usr/lib64/python3.12/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 --record /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/RECORD --output /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-record + rm -fv /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/RECORD removed '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/RECORD' + rm -fv /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/REQUESTED removed '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol-3.1.0.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_FILES_ESCAPE=4.19 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-files --output-modules /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-modules --buildroot /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 --sitelib /usr/lib/python3.12/site-packages --sitearch /usr/lib64/python3.12/site-packages --python-version 3.12 --pyproject-record /builddir/build/BUILD/pymol-3.1.0-13.1.el10.x86_64-pyproject-record --prefix /usr pymol chempy web pymol2 pymol_web pmg_tk pmg_qt + cp -a testing /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/ + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py: updating + echo '#!/bin/sh' + echo 'export PYMOL_PATH=/usr/lib64/python3.12/site-packages/pymol' + echo 'exec /usr/bin/python3 /usr/lib64/python3.12/site-packages/pymol/__init__.py "$@"' + cp -av /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chem_comp_bond-top100.cif' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/setting_help.csv' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/water.pdb' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ace.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/acetylene.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ala.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/arg.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/argn.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asn.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asp.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asph.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpA.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpB.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzene.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl' -> 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'/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hid.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hie.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hip.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/his.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ile.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/indane.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/leu.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lys.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lysn.pkl' 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'/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/realtime.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ser.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/sulfone.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/thr.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trp.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpA.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpB.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl' 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'/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/val.pkl' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate1.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate2.py' 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'/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/__pycache__' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json' -> 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'/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/cmyk.png' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/hsv.ppm' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/splash.png' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/icons' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/icons/icon2.svg' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/matrices' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/matrices/BLOSUM62' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/anaglyph_header.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tsc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tse' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/call_compute_color_for_light.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_color_for_light.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_fog_color.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.gs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.shared' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.fs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.vs' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/README.txt' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__init__.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/apbs.ui' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/creating.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/electrostatics.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/main.py' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/double.png' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single-right.png' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single.png' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/tut' '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb' -> '/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/tut/1hpv.pdb' + _target= + _symlinks=0 + _symlinks=1 + fdupes -q -n -r -p /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chem_comp_bond-top100.cif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chem_comp_bond-top100.cif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/setting_help.csv + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/setting_help.csv + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/water.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/water.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/water.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/water.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ace.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ace.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/acetylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/acetylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/butane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/butane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyanide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyanide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ethylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ethylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formamide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formamide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formic.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formic.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/indane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/indane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methanol.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methanol.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/napthylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/napthylene.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nhh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nhh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nitro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nitro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nme.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nme.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ala.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_arg.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_argn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asph.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_cys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gln.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_glu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gly.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hid.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hie.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hip.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_his.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ile.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_leu.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lys.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_met.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/peptide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/peptide.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phe.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phosphite.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phosphite.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/pro.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/realtime.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/realtime.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ser.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/sulfone.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/sulfone.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/thr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/tyr.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utp.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utpA.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/val.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate1.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate1.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate2.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate2.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_library.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_library.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/Makefile.delsci + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/Makefile.delsci + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/chempy.prm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/chempy.prm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make99_simple.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make99_simple.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make_simple.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make_simple.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_simple.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_simple.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_wld.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_wld.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.dat + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.dat + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.inp + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.inp + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/1hpv.r3d + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1hpv.r3d /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/1hpv.r3d + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/1tii.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/1tii.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/1tii.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/1tii.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/cgo03.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/cgo03.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/cgo03.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/cgo03.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/cgo03.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/cgo03.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/il2.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/il2.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/il2.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/il2.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pkl + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/actions.json + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/actions.json + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/bindings_vive_controller.json + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/bindings_vive_controller.json + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.svg + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.svg + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/icons/refresh.svg + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/icons/refresh.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/styles/pymol.sty + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/styles/pymol.sty + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/cmyk.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/cmyk.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/hsv.ppm + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/hsv.ppm + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/splash.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/splash.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/icons/icon2.svg + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/icons/icon2.svg + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/matrices/BLOSUM62 + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/pymol/matrices/BLOSUM62 + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/anaglyph_header.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/anaglyph_header.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tsc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tsc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tse + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tse + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/call_compute_color_for_light.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/call_compute_color_for_light.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_color_for_light.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_color_for_light.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_fog_color.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_fog_color.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.gs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.gs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.shared + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.shared + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/default.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/label.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/line.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.fs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.fs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.vs + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.vs + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/README.txt + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/README.txt + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__init__.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__init__.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/apbs.ui + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/apbs.ui + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/creating.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/creating.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/electrostatics.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/electrostatics.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/main.py + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/main.py + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/double.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/double.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single-right.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single-right.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single.png + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/test/single.png + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/tut/1hpv.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/data/tut/1hpv.pdb + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/demo.sdf + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/demo.sdf + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae.gz + test 1 = 1 + ln -sf /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae.gz + read _file + test -z /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz + test -z '' + _target= + continue + read _file + mkdir -p /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin + install -p -m 755 pymol /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin/ + desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/applications /builddir/build/SOURCES/pymol.desktop + mkdir -p /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/pixmaps + install -p -m 644 /builddir/build/SOURCES/pymol.png /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/pixmaps/ + mkdir -p /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/metainfo + install -p -m 644 /builddir/build/SOURCES/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/metainfo/ + appstream-util validate-relax --nonet /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64//usr/share/metainfo/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64//usr/share/metainfo/pymol.appdata.xml: OK + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.1.0-13.1.el10 --unique-debug-suffix -3.1.0-13.1.el10.x86_64 --unique-debug-src-base pymol-3.1.0-13.1.el10.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pymol-open-source-3.1.0 find-debuginfo: starting Extracting debug info from 2 files DWARF-compressing 2 files sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/pymol-3.1.0-13.1.el10.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/pymol-3.1.0-13.1.el10.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-13.1.el10.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-13.1.el10.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-13.1.el10.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit mangling shebang in /usr/bin/pymol from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12 using python3.12 /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: invalid escape sequence '\=' /usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: invalid escape sequence '\=' + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Ut31oF + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 + PATH=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib/python3.12/site-packages + _PYTHONSITE=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + /usr/bin/python3 -sP /usr/lib/rpm/redhat/import_all_modules.py -t pymol chempy web pymol2 pymol_web pmg_tk pmg_qt Check import: pymol Check import: chempy Check import: web Check import: pymol2 Check import: pymol_web Check import: pmg_tk Check import: pmg_qt + RPM_EC=0 ++ jobs -p + exit 0 Processing files: pymol-3.1.0-13.1.el10.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.K5jzzP + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-3.1.0 + DOCDIR=/builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-open-source-3.1.0/AUTHORS /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-open-source-3.1.0/DEVELOPERS /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-open-source-3.1.0/README.md /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-open-source-3.1.0/ChangeLog /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64/usr/share/doc/pymol + RPM_EC=0 ++ jobs -p + exit 0 warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chem_comp_bond-top100.cif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ace.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/acetylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/butane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_phe.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_pro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ser.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_thr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_trp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_val.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyanide.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ethylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formamide.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formic.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/indane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methanol.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/napthylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nhh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nitro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nme.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_phe.pkl -> 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/usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/call_compute_color_for_light.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_color_for_light.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_fog_color.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.gs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.shared -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/default.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/default.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/label.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/label.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/line.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/line.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/README.txt -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__init__.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/apbs.ui -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/creating.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/electrostatics.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/main.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/double.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/single-right.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/single.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/tut/1hpv.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/demo.sdf -> /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/1tii.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/il2.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf -> /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/water.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb Provides: PyMOL = 3.1.0-13.1.el10 application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 3.1.0-13.1.el10 pymol(x86-64) = 3.1.0-13.1.el10 python-pymol = 3.1.0-13.1.el10 python3-pymol = 3.1.0-13.1.el10 python3.12-pymol = 3.1.0-13.1.el10 python3.12dist(pymol) = 3.1 python3dist(pymol) = 3.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: (python3.12dist(numpy) < 3~~ with python3.12dist(numpy) >= 1.26.4) /usr/bin/sh libGL.so.1()(64bit) libGLEW.so.2.2()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.35)(64bit) libm.so.6(GLIBC_2.38)(64bit) libnetcdf.so.19()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: python3.12-pymol < 3.1.0-13.1.el10 Processing files: pymol+tests-3.1.0-13.1.el10.x86_64 warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae -> /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms warning: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae.gz -> /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz Provides: pymol+tests = 3.1.0-13.1.el10 pymol+tests(x86-64) = 3.1.0-13.1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/python3 python(abi) = 3.12 Processing files: pymol-debugsource-3.1.0-13.1.el10.x86_64 Provides: pymol-debugsource = 3.1.0-13.1.el10 pymol-debugsource(x86-64) = 3.1.0-13.1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-3.1.0-13.1.el10.x86_64 Provides: debuginfo(build-id) = 64985677de87935b0c6d687dfaff2fe1f869a6e0 debuginfo(build-id) = da7aab21b1c231413c0d4e674eba2baa27facd9c pymol-debuginfo = 3.1.0-13.1.el10 pymol-debuginfo(x86-64) = 3.1.0-13.1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(x86-64) = 3.1.0-13.1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 Wrote: /builddir/build/SRPMS/pymol-3.1.0-13.1.el10.src.rpm Wrote: /builddir/build/RPMS/pymol-3.1.0-13.1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/pymol+tests-3.1.0-13.1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-3.1.0-13.1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-3.1.0-13.1.el10.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.8eI4g2 + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-3.1.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/pymol-3.1.0-13.1.el10.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Ns3htp + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/pymol-open-source-3.1.0-SPECPARTS + rm -rf pymol-open-source-3.1.0 pymol-open-source-3.1.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chem_comp_bond-top100.cif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ace.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/acetylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/butane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_phe.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_pro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_ser.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_thr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_trp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ct_val.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyanide.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ethylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formamide.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/formic.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/indane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/methanol.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/napthylene.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nhh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nitro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nme.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ala.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_arg.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_argn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_asph.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_cys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gln.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_glu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_gly.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hid.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hie.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_hip.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_his.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ile.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_leu.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lys.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_met.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_phe.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_pro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_ser.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_thr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_trp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/nt_val.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/peptide.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phe.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/phosphite.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/pro.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/realtime.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ser.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/sulfone.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/thr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/trp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/tyr.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utp.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/utpA.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/fragments/val.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate1.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/generate2.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/sidechains/sc_library.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/Makefile.delsci -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/chempy.prm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make99_simple.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/make_simple.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_simple.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm99_wld.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.dat -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/tinker/parm_simple.inp -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/chempy/water.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/1hpv.r3d -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1hpv.r3d absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/1tii.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/cgo03.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/cgo03.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/il2.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/demo/pept.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/actions.json -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/actions.json absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/bindings_vive_controller.json -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/hints_vive_controller.svg -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/openvr/menu_splash.svg -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/icons/refresh.svg -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_qt/styles/pymol.sty -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pymol/cmyk.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/cmyk.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pymol/hsv.ppm -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/hsv.ppm absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pymol/icons/icon2.svg -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pymol/matrices/BLOSUM62 -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/pymol/splash.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/pymol/splash.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/setting_help.csv -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/setting_help.csv absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/anaglyph_header.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tsc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tsc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.tse -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.tse absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bezier.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bezier.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/bg.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/bg.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/call_compute_color_for_light.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_color_for_light.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/compute_fog_color.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.gs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.gs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.shared -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.shared absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/connector.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/connector.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/copy.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/copy.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/cylinder.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/cylinder.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/default.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/default.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/default.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/indicator.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/indicator.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/label.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/label.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/label.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/line.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/line.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/line.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/oit.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/oit.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/ramp.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/ramp.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/screen.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/screen.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/sphere.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/sphere.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/surface.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/surface.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/trilines.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/trilines.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/volume.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/volume.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/vrcontroller.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.fs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/shaders/webgl_header.vs -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/README.txt -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/README.txt absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__init__.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/apbs.ui -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/creating.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/electrostatics.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-312.pyc absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/startup/lightingsettings_gui/main.py -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/double.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/double.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/single-right.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single-right.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/test/single.png -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/test/single.png absolute symlink: /usr/lib64/python3.12/site-packages/pymol/data/tut/1hpv.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/tut/1hpv.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/examples/devel/demo.sdf -> /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/1tii.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/1tii.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/il2.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/il2.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf -> /usr/lib64/python3.12/site-packages/pymol/testing/data/ligs3d.sdf absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/pept.pkl -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/demo/pept.pkl absolute symlink: /usr/lib64/python3.12/site-packages/pymol/pymol_path/test/dat/water.pdb -> /usr/lib64/python3.12/site-packages/pymol/pymol_path/data/chempy/water.pdb absolute symlink: /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae -> /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms absolute symlink: /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.mae.gz -> /usr/lib64/python3.12/site-packages/pymol/testing/tests/api/data/foo.cms.gz Finish: rpmbuild pymol-3.1.0-13.1.el10.src.rpm Finish: build phase for pymol-3.1.0-13.1.el10.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-10-x86_64-1766135395.026526/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/pymol-3.1.0-13.1.el10.src.rpm) Config(child) 5 minutes 32 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "13.1.el10", "arch": "src" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "13.1.el10", "arch": "x86_64" }, { "name": "pymol+tests", "epoch": null, "version": "3.1.0", "release": "13.1.el10", "arch": "x86_64" }, { "name": "pymol-debuginfo", "epoch": null, "version": "3.1.0", "release": "13.1.el10", "arch": "x86_64" }, { "name": "pymol-debugsource", "epoch": null, "version": "3.1.0", "release": "13.1.el10", "arch": "x86_64" } ] } RPMResults finished