Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c290' (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/8604335-fedora-41-ppc64le --chroot fedora-41-ppc64le Version: 1.2 PID: 8915 Logging PID: 8916 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8604335, 'buildroot_pkgs': [], 'chroot': 'fedora-41-ppc64le', 'enable_net': False, 'fedora_review': False, 'git_hash': '4e077b05abebc5ef6123cf3c84c782e2d83a6233', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/pymol', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'pymol', 'package_version': '3.1.0-3', 'project_dirname': 'openblas-0.3.23', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-41-ppc64le/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/sergiomb', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': None, 'submitter': 'https://src.fedoraproject.org/user/sergiomb', 'tags': [], 'task_id': '8604335-fedora-41-ppc64le', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/pymol /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/pymol', '/var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol'... Running: git checkout 4e077b05abebc5ef6123cf3c84c782e2d83a6233 -- cmd: ['git', 'checkout', '4e077b05abebc5ef6123cf3c84c782e2d83a6233', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol rc: 0 stdout: stderr: Note: switching to '4e077b05abebc5ef6123cf3c84c782e2d83a6233'. 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 4e077b0 automatic import of pymol Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/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/psimovec/openblas-0.3.23/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 48.0M 0 --:--:-- --:--:-- --:--:-- 48.0M 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/psimovec/openblas-0.3.23/pymol/pymol.png/md5/3bbd85dbd40f588f505ad988b6df2933/pymol.png % Total % Received % Xferd Average Speed Time Time Time Current /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Dload Upload Total Spent Left Speed 100 19466 100 19466 0 0 286k 0 --:--:-- --:--:-- --:--:-- 288k INFO: Reading stdout from command: md5sum pymol.png Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738674685.498307 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-o7wyz67w/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738674685.498307 -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-o7wyz67w/pymol/pymol.spec) Config(fedora-41-ppc64le) Start: clean chroot Finish: clean chroot Mock Version: 6.0 INFO: Mock Version: 6.0 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-ppc64le-bootstrap-1738674685.498307/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.fedoraproject.org/fedora:41 INFO: Pulling image: registry.fedoraproject.org/fedora:41 INFO: Tagging container image as mock-bootstrap-a41e39da-2e36-4dce-96b9-2aed838fddec INFO: Checking that b1134dcde4ca0219a570230c33370fc38648bbabfeba79dd861b172f2858a096 image matches host's architecture INFO: Copy content of container b1134dcde4ca0219a570230c33370fc38648bbabfeba79dd861b172f2858a096 to /var/lib/mock/fedora-41-ppc64le-bootstrap-1738674685.498307/root INFO: mounting b1134dcde4ca0219a570230c33370fc38648bbabfeba79dd861b172f2858a096 with podman image mount INFO: image b1134dcde4ca0219a570230c33370fc38648bbabfeba79dd861b172f2858a096 as /var/lib/containers/storage/overlay/79748acb86cbac1645e1432a9848e0bed2e18ab0985e742c22fd00ec84ace215/merged INFO: umounting image b1134dcde4ca0219a570230c33370fc38648bbabfeba79dd861b172f2858a096 (/var/lib/containers/storage/overlay/79748acb86cbac1645e1432a9848e0bed2e18ab0985e742c22fd00ec84ace215/merged) with podman image umount INFO: Removing image mock-bootstrap-a41e39da-2e36-4dce-96b9-2aed838fddec INFO: Package manager dnf5 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/fedora-41-ppc64le-1738674685.498307/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 dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.ppc64le rpm-sequoia-1.7.0-3.fc41.ppc64le dnf5-5.2.8.1-3.fc41.ppc64le dnf5-plugins-5.2.8.1-3.fc41.ppc64le Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 6.6 MiB/s | 8.4 MiB | 00m01s fedora 100% | 7.9 MiB/s | 33.3 MiB | 00m04s Copr repository 100% | 17.4 MiB/s | 3.1 MiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 45.4 MiB/s | 13.9 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash ppc64le 5.2.37-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.7 MiB bzip2 ppc64le 1.0.8-20.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 171.1 KiB coreutils ppc64le 9.6-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.4 MiB cpio ppc64le 2.15-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB diffutils ppc64le 3.10-9.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB fedora-release-common noarch 42-0.16 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19.8 KiB findutils ppc64le 1:4.10.0-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB gawk ppc64le 5.3.1-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.7 MiB glibc-minimal-langpack ppc64le 2.40.9000-35.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B grep ppc64le 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ppc64le 2.40.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.7 MiB which ppc64le 2.23-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 123.3 KiB xz ppc64le 1:5.6.3-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 MiB Installing dependencies: add-determinism ppc64le 0.5.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.5 MiB alternatives ppc64le 1.31-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 90.1 KiB ansible-srpm-macros noarch 1-17.1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 35.7 KiB audit-libs ppc64le 4.0.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 479.0 KiB authselect ppc64le 1.5.0-9.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 179.8 KiB authselect-libs ppc64le 1.5.0-9.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 865.4 KiB basesystem noarch 11-22.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B binutils ppc64le 2.43.50-12.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31.2 MiB build-reproducibility-srpm-macros noarch 0.5.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 735.0 B bzip2-libs ppc64le 1.0.8-20.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 136.5 KiB ca-certificates noarch 2024.2.69_v8.0.401-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.6 MiB coreutils-common ppc64le 9.6-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11.1 MiB cracklib ppc64le 2.9.11-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 421.7 KiB crypto-policies noarch 20250124-1.git4d262e7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 137.4 KiB curl ppc64le 8.11.1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 518.7 KiB cyrus-sasl-lib ppc64le 2.1.28-30.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 MiB dbus ppc64le 1:1.16.0-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B dbus-broker ppc64le 36-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549.8 KiB dbus-common noarch 1:1.16.0-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11.2 KiB debugedit ppc64le 5.1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 308.1 KiB dwz ppc64le 0.15-9.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 386.6 KiB ed ppc64le 1.21-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 154.4 KiB efi-srpm-macros noarch 6-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40.1 KiB elfutils ppc64le 0.192-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.4 MiB elfutils-debuginfod-client ppc64le 0.192-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 143.5 KiB elfutils-default-yama-scope noarch 0.192-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 KiB elfutils-libelf ppc64le 0.192-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB elfutils-libs ppc64le 0.192-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 874.2 KiB expat ppc64le 2.6.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 348.5 KiB fedora-gpg-keys noarch 42-0.4 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 128.2 KiB fedora-release noarch 42-0.16 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B fedora-release-identity-basic noarch 42-0.16 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 719.0 B fedora-repos noarch 42-0.4 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.9 KiB fedora-repos-rawhide noarch 42-0.4 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 KiB file ppc64le 5.46-1.fc42 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB openblas-srpm-macros noarch 2-19.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112.0 B openldap ppc64le 2.6.9-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 889.2 KiB openssl-libs ppc64le 1:3.2.2-14.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 MiB p11-kit ppc64le 0.25.5-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.8 MiB p11-kit-trust ppc64le 0.25.5-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 527.1 KiB package-notes-srpm-macros noarch 0.5-13.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 KiB pam ppc64le 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.2 MiB pam-libs ppc64le 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 286.2 KiB pcre2 ppc64le 10.44-1.fc42.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 776.5 KiB pcre2-syntax noarch 10.44-1.fc42.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251.6 KiB perl-srpm-macros noarch 1-57.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0 B pkgconf ppc64le 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112.4 KiB pkgconf-m4 noarch 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14.4 KiB pkgconf-pkg-config ppc64le 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 990.0 B popt ppc64le 1.19-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 208.7 KiB publicsuffix-list-dafsa noarch 20250116-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 68.5 KiB pyproject-srpm-macros noarch 1.16.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB python-srpm-macros noarch 3.13-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 500.0 B qt6-srpm-macros noarch 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0 B readline ppc64le 8.2-12.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 624.9 KiB rpm ppc64le 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.1 MiB rpm-build-libs ppc64le 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.5 KiB rpm-libs ppc64le 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 989.8 KiB rpm-sequoia ppc64le 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.8 MiB rust-srpm-macros noarch 26.3-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.8 KiB setup noarch 2.15.0-10.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.7 KiB sqlite-libs ppc64le 3.47.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 MiB systemd ppc64le 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22.3 MiB systemd-libs ppc64le 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 MiB systemd-pam ppc64le 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 MiB systemd-rpm-macros noarch 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10.7 KiB tree-sitter-srpm-macros noarch 0.1.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.5 KiB util-linux-core ppc64le 2.40.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.5 MiB xxhash-libs ppc64le 0.8.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85.6 KiB xz-libs ppc64le 1:5.6.3-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 266.0 KiB zig-srpm-macros noarch 1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 KiB zip ppc64le 3.0-43.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 889.8 KiB zlib-ng-compat ppc64le 2.2.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.4 KiB zstd ppc64le 1.5.6-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 164 packages Total size of inbound packages is 64 MiB. Need to download 64 MiB. After this operation, 259 MiB extra will be used (install 259 MiB, remove 0 B). [ 1/164] bzip2-0:1.0.8-20.fc42.ppc64le 100% | 665.6 KiB/s | 53.2 KiB | 00m00s [ 2/164] bash-0:5.2.37-1.fc42.ppc64le 100% | 15.0 MiB/s | 1.9 MiB | 00m00s [ 3/164] coreutils-0:9.6-1.fc42.ppc64l 100% | 9.1 MiB/s | 1.2 MiB | 00m00s [ 4/164] cpio-0:2.15-2.fc41.ppc64le 100% | 5.3 MiB/s | 292.9 KiB | 00m00s [ 5/164] diffutils-0:3.10-9.fc42.ppc64 100% | 13.3 MiB/s | 409.1 KiB | 00m00s [ 6/164] fedora-release-common-0:42-0. 100% | 1.1 MiB/s | 24.3 KiB | 00m00s [ 7/164] findutils-1:4.10.0-5.fc42.ppc 100% | 16.7 MiB/s | 580.5 KiB | 00m00s [ 8/164] glibc-minimal-langpack-0:2.40 100% | 5.9 MiB/s | 127.9 KiB | 00m00s [ 9/164] gawk-0:5.3.1-1.fc42.ppc64le 100% | 24.0 MiB/s | 1.1 MiB | 00m00s [ 10/164] grep-0:3.11-10.fc42.ppc64le 100% | 8.6 MiB/s | 299.2 KiB | 00m00s [ 11/164] gzip-0:1.13-3.fc42.ppc64le 100% | 5.9 MiB/s | 168.5 KiB | 00m00s [ 12/164] info-0:7.2-3.fc42.ppc64le 100% | 7.6 MiB/s | 202.7 KiB | 00m00s [ 13/164] redhat-rpm-config-0:342-2.fc4 100% | 3.2 MiB/s | 74.9 KiB | 00m00s [ 14/164] patch-0:2.7.6-26.fc42.ppc64le 100% | 5.2 MiB/s | 139.7 KiB | 00m00s [ 15/164] rpm-build-0:4.20.0-8.fc42.ppc 100% | 3.4 MiB/s | 76.6 KiB | 00m00s [ 16/164] sed-0:4.9-4.fc42.ppc64le 100% | 12.8 MiB/s | 314.2 KiB | 00m00s [ 17/164] shadow-utils-2:4.17.0-4.fc42. 100% | 23.7 MiB/s | 1.3 MiB | 00m00s [ 18/164] unzip-0:6.0-66.fc42.ppc64le 100% | 5.5 MiB/s | 190.9 KiB | 00m00s [ 19/164] tar-2:1.35-5.fc42.ppc64le 100% | 18.3 MiB/s | 878.3 KiB | 00m00s [ 20/164] which-0:2.23-1.fc42.ppc64le 100% | 1.7 MiB/s | 43.0 KiB | 00m00s [ 21/164] xz-1:5.6.3-3.fc42.ppc64le 100% | 18.2 MiB/s | 465.3 KiB | 00m00s [ 22/164] util-linux-0:2.40.4-2.fc42.pp 100% | 25.3 MiB/s | 1.2 MiB | 00m00s [ 23/164] fedora-repos-0:42-0.4.noarch 100% | 515.5 KiB/s | 9.3 KiB | 00m00s [ 24/164] filesystem-0:3.18-36.fc42.ppc 100% | 29.2 MiB/s | 1.3 MiB | 00m00s [ 25/164] coreutils-common-0:9.6-1.fc42 100% | 29.5 MiB/s | 2.1 MiB | 00m00s [ 26/164] glibc-common-0:2.40.9000-35.f 100% | 14.8 MiB/s | 423.8 KiB | 00m00s [ 27/164] filesystem-srpm-macros-0:3.18 100% | 1.3 MiB/s | 25.6 KiB | 00m00s [ 28/164] rpm-0:4.20.0-8.fc42.ppc64le 100% | 18.8 MiB/s | 518.7 KiB | 00m00s [ 29/164] libblkid-0:2.40.4-2.fc42.ppc6 100% | 5.9 MiB/s | 145.4 KiB | 00m00s [ 30/164] glibc-0:2.40.9000-35.fc42.ppc 100% | 30.5 MiB/s | 3.2 MiB | 00m00s [ 31/164] libfdisk-0:2.40.4-2.fc42.ppc6 100% | 5.6 MiB/s | 177.8 KiB | 00m00s [ 32/164] libmount-0:2.40.4-2.fc42.ppc6 100% | 4.0 MiB/s | 181.2 KiB | 00m00s [ 33/164] libsmartcols-0:2.40.4-2.fc42. 100% | 5.4 MiB/s | 111.6 KiB | 00m00s [ 34/164] libuuid-0:2.40.4-2.fc42.ppc64 100% | 1.7 MiB/s | 30.9 KiB | 00m00s [ 35/164] fedora-gpg-keys-0:42-0.4.noar 100% | 6.4 MiB/s | 125.2 KiB | 00m00s [ 36/164] xz-libs-1:5.6.3-3.fc42.ppc64l 100% | 5.6 MiB/s | 126.4 KiB | 00m00s [ 37/164] util-linux-core-0:2.40.4-2.fc 100% | 18.2 MiB/s | 559.3 KiB | 00m00s [ 38/164] fedora-repos-rawhide-0:42-0.4 100% | 421.5 KiB/s | 8.9 KiB | 00m00s [ 39/164] rpm-libs-0:4.20.0-8.fc42.ppc6 100% | 12.0 MiB/s | 357.6 KiB | 00m00s [ 40/164] rpm-build-libs-0:4.20.0-8.fc4 100% | 5.0 MiB/s | 107.6 KiB | 00m00s [ 41/164] libxcrypt-0:4.4.38-4.fc42.ppc 100% | 5.3 MiB/s | 131.3 KiB | 00m00s [ 42/164] glibc-gconv-extra-0:2.40.9000 100% | 23.3 MiB/s | 1.7 MiB | 00m00s [ 43/164] systemd-libs-0:257.2-17.fc42. 100% | 18.5 MiB/s | 871.7 KiB | 00m00s [ 44/164] libselinux-0:3.8-1.fc42.ppc64 100% | 3.6 MiB/s | 111.4 KiB | 00m00s [ 45/164] libsepol-0:3.8-1.fc42.ppc64le 100% | 15.5 MiB/s | 381.1 KiB | 00m00s [ 46/164] ncurses-base-0:6.5-5.20250125 100% | 2.8 MiB/s | 63.5 KiB | 00m00s [ 47/164] ncurses-libs-0:6.5-5.20250125 100% | 13.9 MiB/s | 383.5 KiB | 00m00s [ 48/164] audit-libs-0:4.0.3-2.fc42.ppc 100% | 6.0 MiB/s | 141.1 KiB | 00m00s [ 49/164] libeconf-0:0.7.5-2.fc42.ppc64 100% | 1.9 MiB/s | 39.8 KiB | 00m00s [ 50/164] pam-0:1.7.0-4.fc42.ppc64le 100% | 17.1 MiB/s | 559.8 KiB | 00m00s [ 51/164] pam-libs-0:1.7.0-4.fc42.ppc64 100% | 2.7 MiB/s | 64.4 KiB | 00m00s [ 52/164] zlib-ng-compat-0:2.2.3-2.fc42 100% | 3.4 MiB/s | 80.9 KiB | 00m00s [ 53/164] authselect-0:1.5.0-9.fc42.ppc 100% | 5.5 MiB/s | 141.0 KiB | 00m00s [ 54/164] authselect-libs-0:1.5.0-9.fc4 100% | 6.3 MiB/s | 206.5 KiB | 00m00s [ 55/164] libcap-ng-0:0.8.5-4.fc42.ppc6 100% | 1.4 MiB/s | 33.5 KiB | 00m00s [ 56/164] librtas-0:2.0.6-3.fc42.ppc64l 100% | 3.4 MiB/s | 81.0 KiB | 00m00s [ 57/164] readline-0:8.2-12.fc42.ppc64l 100% | 9.1 MiB/s | 232.0 KiB | 00m00s [ 58/164] bzip2-libs-0:1.0.8-20.fc42.pp 100% | 2.2 MiB/s | 49.5 KiB | 00m00s [ 59/164] libacl-0:2.3.2-3.fc42.ppc64le 100% | 1.1 MiB/s | 25.3 KiB | 00m00s [ 60/164] libgcc-0:15.0.1-0.6.fc42.ppc6 100% | 4.1 MiB/s | 96.5 KiB | 00m00s [ 61/164] libcap-0:2.73-2.fc42.ppc64le 100% | 3.6 MiB/s | 91.8 KiB | 00m00s [ 62/164] setup-0:2.15.0-10.fc42.noarch 100% | 6.6 MiB/s | 149.8 KiB | 00m00s [ 63/164] libsemanage-0:3.8-1.fc42.ppc6 100% | 6.0 MiB/s | 135.2 KiB | 00m00s [ 64/164] rpm-sequoia-0:1.7.0-4.fc42.pp 100% | 24.0 MiB/s | 1.0 MiB | 00m00s [ 65/164] sqlite-libs-0:3.47.2-2.fc42.p 100% | 20.4 MiB/s | 836.3 KiB | 00m00s [ 66/164] libzstd-0:1.5.6-3.fc42.ppc64l 100% | 10.4 MiB/s | 352.2 KiB | 00m00s [ 67/164] lua-libs-0:5.4.7-2.fc42.ppc64 100% | 5.8 MiB/s | 148.8 KiB | 00m00s [ 68/164] popt-0:1.19-8.fc42.ppc64le 100% | 3.0 MiB/s | 63.8 KiB | 00m00s [ 69/164] elfutils-libelf-0:0.192-8.fc4 100% | 8.8 MiB/s | 217.0 KiB | 00m00s [ 70/164] elfutils-libs-0:0.192-8.fc42. 100% | 12.4 MiB/s | 303.6 KiB | 00m00s [ 71/164] elfutils-debuginfod-client-0: 100% | 2.4 MiB/s | 49.6 KiB | 00m00s [ 72/164] elfutils-0:0.192-8.fc42.ppc64 100% | 15.3 MiB/s | 562.8 KiB | 00m00s [ 73/164] libgomp-0:15.0.1-0.6.fc42.ppc 100% | 13.7 MiB/s | 364.3 KiB | 00m00s [ 74/164] file-0:5.46-1.fc42.ppc64le 100% | 2.5 MiB/s | 49.5 KiB | 00m00s [ 75/164] file-libs-0:5.46-1.fc42.ppc64 100% | 21.0 MiB/s | 861.7 KiB | 00m00s [ 76/164] alternatives-0:1.31-3.fc42.pp 100% | 1.9 MiB/s | 43.7 KiB | 00m00s [ 77/164] jansson-0:2.14-2.fc42.ppc64le 100% | 2.3 MiB/s | 50.9 KiB | 00m00s [ 78/164] debugedit-0:5.1-4.fc42.ppc64l 100% | 3.3 MiB/s | 82.3 KiB | 00m00s [ 79/164] libarchive-0:3.7.7-2.fc42.ppc 100% | 17.0 MiB/s | 486.0 KiB | 00m00s [ 80/164] pkgconf-pkg-config-0:2.3.0-2. 100% | 447.8 KiB/s | 9.9 KiB | 00m00s [ 81/164] pkgconf-0:2.3.0-2.fc42.ppc64l 100% | 2.2 MiB/s | 45.5 KiB | 00m00s [ 82/164] pkgconf-m4-0:2.3.0-2.fc42.noa 100% | 837.4 KiB/s | 14.2 KiB | 00m00s [ 83/164] libpkgconf-0:2.3.0-2.fc42.ppc 100% | 1.9 MiB/s | 43.2 KiB | 00m00s [ 84/164] zstd-0:1.5.6-3.fc42.ppc64le 100% | 18.2 MiB/s | 522.6 KiB | 00m00s [ 85/164] binutils-0:2.43.50-12.fc42.pp 100% | 39.8 MiB/s | 6.5 MiB | 00m00s [ 86/164] curl-0:8.11.1-4.fc42.ppc64le 100% | 4.3 MiB/s | 228.1 KiB | 00m00s [ 87/164] build-reproducibility-srpm-ma 100% | 241.8 KiB/s | 11.6 KiB | 00m00s [ 88/164] efi-srpm-macros-0:6-2.fc42.no 100% | 1.2 MiB/s | 22.5 KiB | 00m00s [ 89/164] forge-srpm-macros-0:0.4.0-2.f 100% | 1.1 MiB/s | 19.9 KiB | 00m00s [ 90/164] add-determinism-0:0.5.0-2.fc4 100% | 25.2 MiB/s | 956.5 KiB | 00m00s [ 91/164] go-srpm-macros-0:3.6.0-6.fc42 100% | 1.2 MiB/s | 27.7 KiB | 00m00s [ 92/164] pyproject-srpm-macros-0:1.16. 100% | 738.7 KiB/s | 14.0 KiB | 00m00s [ 93/164] qt6-srpm-macros-0:6.8.2-1.fc4 100% | 417.9 KiB/s | 9.2 KiB | 00m00s [ 94/164] tree-sitter-srpm-macros-0:0.1 100% | 624.0 KiB/s | 11.2 KiB | 00m00s [ 95/164] ansible-srpm-macros-0:1-17.1. 100% | 967.4 KiB/s | 20.3 KiB | 00m00s [ 96/164] fonts-srpm-macros-1:2.0.5-21. 100% | 1.4 MiB/s | 27.1 KiB | 00m00s [ 97/164] dwz-0:0.15-9.fc42.ppc64le 100% | 6.5 MiB/s | 145.6 KiB | 00m00s [ 98/164] fpc-srpm-macros-0:1.3-14.fc42 100% | 445.5 KiB/s | 8.0 KiB | 00m00s [ 99/164] ghc-srpm-macros-0:1.9.2-2.fc4 100% | 538.6 KiB/s | 9.2 KiB | 00m00s [100/164] gnat-srpm-macros-0:6-7.fc42.n 100% | 506.5 KiB/s | 8.6 KiB | 00m00s [101/164] kernel-srpm-macros-0:1.0-25.f 100% | 580.7 KiB/s | 9.9 KiB | 00m00s [102/164] lua-srpm-macros-0:1-15.fc42.n 100% | 524.5 KiB/s | 8.9 KiB | 00m00s [103/164] ocaml-srpm-macros-0:10-4.fc42 100% | 541.5 KiB/s | 9.2 KiB | 00m00s [104/164] openblas-srpm-macros-0:2-19.f 100% | 485.4 KiB/s | 7.8 KiB | 00m00s [105/164] package-notes-srpm-macros-0:0 100% | 544.7 KiB/s | 9.3 KiB | 00m00s [106/164] perl-srpm-macros-0:1-57.fc42. 100% | 500.3 KiB/s | 8.5 KiB | 00m00s [107/164] python-srpm-macros-0:3.13-4.f 100% | 1.3 MiB/s | 23.0 KiB | 00m00s [108/164] qt5-srpm-macros-0:5.15.15-1.f 100% | 523.4 KiB/s | 8.9 KiB | 00m00s [109/164] rust-srpm-macros-0:26.3-4.fc4 100% | 616.1 KiB/s | 11.7 KiB | 00m00s [110/164] zig-srpm-macros-0:1-4.fc42.no 100% | 458.0 KiB/s | 8.2 KiB | 00m00s [111/164] zip-0:3.0-43.fc42.ppc64le 100% | 9.0 MiB/s | 275.5 KiB | 00m00s [112/164] libattr-0:2.5.2-5.fc42.ppc64l 100% | 797.7 KiB/s | 17.5 KiB | 00m00s [113/164] ed-0:1.21-2.fc42.ppc64le 100% | 3.2 MiB/s | 85.2 KiB | 00m00s [114/164] libtirpc-0:1.3.6-1.rc3.fc42.2 100% | 4.3 MiB/s | 109.6 KiB | 00m00s [115/164] gdbm-1:1.23-9.fc42.ppc64le 100% | 5.2 MiB/s | 154.6 KiB | 00m00s [116/164] gdbm-libs-1:1.23-9.fc42.ppc64 100% | 3.2 MiB/s | 61.8 KiB | 00m00s [117/164] libpwquality-0:1.4.5-12.fc42. 100% | 4.9 MiB/s | 110.2 KiB | 00m00s [118/164] openssl-libs-1:3.2.2-14.fc42. 100% | 36.3 MiB/s | 2.5 MiB | 00m00s [119/164] crypto-policies-0:20250124-1. 100% | 3.0 MiB/s | 73.6 KiB | 00m00s [120/164] ca-certificates-0:2024.2.69_v 100% | 23.7 MiB/s | 945.0 KiB | 00m00s [121/164] libcom_err-0:1.47.2-3.fc42.pp 100% | 1.2 MiB/s | 27.3 KiB | 00m00s [122/164] krb5-libs-0:1.21.3-5.fc42.ppc 100% | 23.6 MiB/s | 847.1 KiB | 00m00s [123/164] pcre2-syntax-0:10.44-1.fc42.2 100% | 7.7 MiB/s | 149.8 KiB | 00m00s [124/164] pcre2-0:10.44-1.fc42.2.ppc64l 100% | 11.3 MiB/s | 254.3 KiB | 00m00s [125/164] cracklib-0:2.9.11-7.fc42.ppc6 100% | 3.7 MiB/s | 83.0 KiB | 00m00s [126/164] lz4-libs-0:1.10.0-2.fc42.ppc6 100% | 4.7 MiB/s | 102.1 KiB | 00m00s [127/164] libxml2-0:2.12.9-2.fc42.ppc64 100% | 23.7 MiB/s | 776.5 KiB | 00m00s [128/164] keyutils-libs-0:1.6.3-5.fc42. 100% | 1.7 MiB/s | 32.7 KiB | 00m00s [129/164] libverto-0:0.3.2-10.fc42.ppc6 100% | 1.1 MiB/s | 22.1 KiB | 00m00s [130/164] basesystem-0:11-22.fc42.noarc 100% | 428.8 KiB/s | 7.3 KiB | 00m00s [131/164] gmp-1:6.3.0-2.fc41.ppc64le 100% | 15.1 MiB/s | 309.0 KiB | 00m00s [132/164] mpfr-0:4.2.1-6.fc42.ppc64le 100% | 14.7 MiB/s | 362.4 KiB | 00m00s [133/164] elfutils-default-yama-scope-0 100% | 699.8 KiB/s | 12.6 KiB | 00m00s [134/164] json-c-0:0.18-2.fc42.ppc64le 100% | 2.5 MiB/s | 49.3 KiB | 00m00s [135/164] libffi-0:3.4.6-5.fc42.ppc64le 100% | 2.1 MiB/s | 38.7 KiB | 00m00s [136/164] p11-kit-0:0.25.5-5.fc42.ppc64 100% | 21.3 MiB/s | 479.5 KiB | 00m00s [137/164] libstdc++-0:15.0.1-0.6.fc42.p 100% | 29.6 MiB/s | 1.0 MiB | 00m00s [138/164] p11-kit-trust-0:0.25.5-5.fc42 100% | 6.3 MiB/s | 149.0 KiB | 00m00s [139/164] systemd-rpm-macros-0:257.2-17 100% | 2.0 MiB/s | 34.9 KiB | 00m00s [140/164] systemd-pam-0:257.2-17.fc42.p 100% | 18.1 MiB/s | 445.2 KiB | 00m00s [141/164] libtasn1-0:4.19.0-11.fc42.ppc 100% | 3.4 MiB/s | 80.2 KiB | 00m00s [142/164] dbus-1:1.16.0-3.fc42.ppc64le 100% | 451.6 KiB/s | 7.7 KiB | 00m00s [143/164] libseccomp-0:2.5.5-2.fc41.ppc 100% | 3.6 MiB/s | 78.4 KiB | 00m00s [144/164] dbus-broker-0:36-5.fc42.ppc64 100% | 8.1 MiB/s | 191.7 KiB | 00m00s [145/164] expat-0:2.6.4-2.fc42.ppc64le 100% | 5.9 MiB/s | 120.7 KiB | 00m00s [146/164] dbus-common-1:1.16.0-3.fc42.n 100% | 850.2 KiB/s | 14.5 KiB | 00m00s [147/164] fedora-release-0:42-0.16.noar 100% | 746.1 KiB/s | 13.4 KiB | 00m00s [148/164] systemd-0:257.2-17.fc42.ppc64 100% | 42.7 MiB/s | 5.9 MiB | 00m00s [149/164] fedora-release-identity-basic 100% | 339.0 KiB/s | 14.2 KiB | 00m00s [150/164] libcurl-0:8.11.1-4.fc42.ppc64 100% | 18.0 MiB/s | 423.1 KiB | 00m00s [151/164] libnghttp2-0:1.64.0-3.fc42.pp 100% | 4.4 MiB/s | 86.1 KiB | 00m00s [152/164] libssh-0:0.11.1-4.fc42.ppc64l 100% | 12.3 MiB/s | 264.9 KiB | 00m00s [153/164] libssh-config-0:0.11.1-4.fc42 100% | 562.7 KiB/s | 9.0 KiB | 00m00s [154/164] xxhash-libs-0:0.8.3-2.fc42.pp 100% | 1.8 MiB/s | 38.1 KiB | 00m00s [155/164] openldap-0:2.6.9-3.fc42.ppc64 100% | 13.5 MiB/s | 289.4 KiB | 00m00s [156/164] libidn2-0:2.3.7-3.fc42.ppc64l 100% | 5.6 MiB/s | 114.9 KiB | 00m00s [157/164] libbrotli-0:1.1.0-6.fc42.ppc6 100% | 15.6 MiB/s | 382.4 KiB | 00m00s [158/164] gdb-minimal-0:15.2-7.fc42.ppc 100% | 28.7 MiB/s | 4.6 MiB | 00m00s [159/164] libpsl-0:0.21.5-5.fc42.ppc64l 100% | 2.2 MiB/s | 65.8 KiB | 00m00s [160/164] cyrus-sasl-lib-0:2.1.28-30.fc 100% | 22.6 MiB/s | 880.8 KiB | 00m00s [161/164] libtool-ltdl-0:2.5.4-4.fc42.p 100% | 1.8 MiB/s | 39.4 KiB | 00m00s [162/164] libevent-0:2.1.12-15.fc42.ppc 100% | 11.7 MiB/s | 275.3 KiB | 00m00s [163/164] publicsuffix-list-dafsa-0:202 100% | 2.9 MiB/s | 58.8 KiB | 00m00s [164/164] libunistring-0:1.1-9.fc42.ppc 100% | 18.8 MiB/s | 577.8 KiB | 00m00s -------------------------------------------------------------------------------- [164/164] Total 100% | 36.7 MiB/s | 63.9 MiB | 00m02s Running transaction [ 1/166] Verify package files 100% | 231.0 B/s | 164.0 B | 00m01s >>> Running pre-transaction scriptlet: filesystem-0:3.18-36.fc42.ppc64le >>> Finished pre-transaction scriptlet: filesystem-0:3.18-36.fc42.ppc64le >>> [RPM] /var/lib/mock/fedora-41-ppc64le-1738674685.498307/root/var/cache/dnf/c [ 2/166] Prepare transaction 100% | 1.3 KiB/s | 164.0 B | 00m00s [ 3/166] Installing libgcc-0:15.0.1-0. 100% | 70.3 MiB/s | 288.1 KiB | 00m00s [ 4/166] Installing publicsuffix-list- 100% | 67.6 MiB/s | 69.2 KiB | 00m00s [ 5/166] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 6/166] Installing fedora-release-ide 100% | 0.0 B/s | 976.0 B | 00m00s [ 7/166] Installing fedora-repos-rawhi 100% | 2.4 MiB/s | 2.4 KiB | 00m00s [ 8/166] Installing fedora-gpg-keys-0: 100% | 17.1 MiB/s | 174.8 KiB | 00m00s [ 9/166] Installing fedora-repos-0:42- 100% | 5.6 MiB/s | 5.7 KiB | 00m00s [ 10/166] Installing fedora-release-com 100% | 11.8 MiB/s | 24.1 KiB | 00m00s [ 11/166] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s [ 12/166] Installing setup-0:2.15.0-10. 100% | 24.5 MiB/s | 726.5 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/166] Installing filesystem-0:3.18- 100% | 1.1 MiB/s | 212.4 KiB | 00m00s [ 14/166] Installing basesystem-0:11-22 100% | 0.0 B/s | 124.0 B | 00m00s [ 15/166] Installing pcre2-syntax-0:10. 100% | 82.7 MiB/s | 254.1 KiB | 00m00s [ 16/166] Installing rust-srpm-macros-0 100% | 5.4 MiB/s | 5.6 KiB | 00m00s [ 17/166] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [ 18/166] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [ 19/166] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [ 20/166] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [ 21/166] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [ 22/166] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [ 23/166] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [ 24/166] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [ 25/166] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [ 26/166] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [ 27/166] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [ 28/166] Installing pkgconf-m4-0:2.3.0 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [ 29/166] Installing ncurses-base-0:6.5 100% | 26.5 MiB/s | 352.2 KiB | 00m00s [ 30/166] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 31/166] Installing ncurses-libs-0:6.5 100% | 115.1 MiB/s | 1.5 MiB | 00m00s [ 32/166] Installing glibc-0:2.40.9000- 100% | 114.7 MiB/s | 11.7 MiB | 00m00s [ 33/166] Installing bash-0:5.2.37-1.fc 100% | 111.2 MiB/s | 8.7 MiB | 00m00s [ 34/166] Installing glibc-common-0:2.4 100% | 42.0 MiB/s | 1.5 MiB | 00m00s [ 35/166] Installing glibc-gconv-extra- 100% | 160.1 MiB/s | 18.6 MiB | 00m00s [ 36/166] Installing zlib-ng-compat-0:2 100% | 96.8 MiB/s | 198.2 KiB | 00m00s [ 37/166] Installing xz-libs-1:5.6.3-3. 100% | 130.4 MiB/s | 267.1 KiB | 00m00s [ 38/166] Installing bzip2-libs-0:1.0.8 100% | 67.2 MiB/s | 137.6 KiB | 00m00s [ 39/166] Installing libuuid-0:2.40.4-2 100% | 68.6 MiB/s | 70.2 KiB | 00m00s [ 40/166] Installing libblkid-0:2.40.4- 100% | 115.8 MiB/s | 355.6 KiB | 00m00s [ 41/166] Installing libxcrypt-0:4.4.38 100% | 82.6 MiB/s | 338.4 KiB | 00m00s [ 42/166] Installing readline-0:8.2-12. 100% | 122.5 MiB/s | 627.0 KiB | 00m00s [ 43/166] Installing popt-0:1.19-8.fc42 100% | 35.0 MiB/s | 215.3 KiB | 00m00s [ 44/166] Installing libzstd-0:1.5.6-3. 100% | 150.5 MiB/s | 924.9 KiB | 00m00s [ 45/166] Installing elfutils-libelf-0: 100% | 156.5 MiB/s | 1.3 MiB | 00m00s [ 46/166] Installing gmp-1:6.3.0-2.fc41 100% | 138.8 MiB/s | 852.5 KiB | 00m00s [ 47/166] Installing libstdc++-0:15.0.1 100% | 159.9 MiB/s | 3.8 MiB | 00m00s [ 48/166] Installing libeconf-0:0.7.5-2 100% | 40.1 MiB/s | 82.1 KiB | 00m00s [ 49/166] Installing libcap-ng-0:0.8.5- 100% | 79.2 MiB/s | 162.1 KiB | 00m00s [ 50/166] Installing audit-libs-0:4.0.3 100% | 117.5 MiB/s | 481.1 KiB | 00m00s [ 51/166] Installing pam-libs-0:1.7.0-4 100% | 93.9 MiB/s | 288.6 KiB | 00m00s [ 52/166] Installing libcap-0:2.73-2.fc 100% | 19.2 MiB/s | 510.6 KiB | 00m00s [ 53/166] Installing systemd-libs-0:257 100% | 152.5 MiB/s | 2.9 MiB | 00m00s [ 54/166] Installing libattr-0:2.5.2-5. 100% | 66.2 MiB/s | 67.7 KiB | 00m00s [ 55/166] Installing libacl-0:2.3.2-3.f 100% | 65.2 MiB/s | 66.8 KiB | 00m00s [ 56/166] Installing gdbm-libs-1:1.23-9 100% | 114.8 MiB/s | 235.2 KiB | 00m00s [ 57/166] Installing mpfr-0:4.2.1-6.fc4 100% | 127.6 MiB/s | 914.4 KiB | 00m00s [ 58/166] Installing gawk-0:5.3.1-1.fc4 100% | 65.9 MiB/s | 2.7 MiB | 00m00s [ 59/166] Installing dwz-0:0.15-9.fc42. 100% | 15.8 MiB/s | 388.0 KiB | 00m00s [ 60/166] Installing libfdisk-0:2.40.4- 100% | 118.2 MiB/s | 484.1 KiB | 00m00s [ 61/166] Installing unzip-0:6.0-66.fc4 100% | 20.2 MiB/s | 537.4 KiB | 00m00s [ 62/166] Installing file-libs-0:5.46-1 100% | 228.5 MiB/s | 11.9 MiB | 00m00s [ 63/166] Installing file-0:5.46-1.fc42 100% | 5.1 MiB/s | 141.6 KiB | 00m00s [ 64/166] Installing crypto-policies-0: 100% | 13.3 MiB/s | 163.7 KiB | 00m00s [ 65/166] Installing libsmartcols-0:2.4 100% | 94.5 MiB/s | 290.4 KiB | 00m00s [ 66/166] Installing libsepol-0:3.8-1.f 100% | 130.3 MiB/s | 1.0 MiB | 00m00s [ 67/166] Installing lua-libs-0:5.4.7-2 100% | 128.3 MiB/s | 394.0 KiB | 00m00s [ 68/166] Installing alternatives-0:1.3 100% | 3.9 MiB/s | 91.6 KiB | 00m00s [ 69/166] Installing libcom_err-0:1.47. 100% | 54.8 MiB/s | 112.1 KiB | 00m00s [ 70/166] Installing pcre2-0:10.44-1.fc 100% | 126.6 MiB/s | 777.9 KiB | 00m00s [ 71/166] Installing libselinux-0:3.8-1 100% | 86.7 MiB/s | 266.3 KiB | 00m00s [ 72/166] Installing grep-0:3.11-10.fc4 100% | 30.4 MiB/s | 1.0 MiB | 00m00s [ 73/166] Installing sed-0:4.9-4.fc42.p 100% | 28.8 MiB/s | 945.3 KiB | 00m00s [ 74/166] Installing findutils-1:4.10.0 100% | 53.8 MiB/s | 2.0 MiB | 00m00s [ 75/166] Installing libmount-0:2.40.4- 100% | 94.7 MiB/s | 485.0 KiB | 00m00s [ 76/166] Installing util-linux-core-0: 100% | 58.3 MiB/s | 2.5 MiB | 00m00s [ 77/166] Installing xz-1:5.6.3-3.fc42. 100% | 35.7 MiB/s | 1.3 MiB | 00m00s [ 78/166] Installing lz4-libs-0:1.10.0- 100% | 85.4 MiB/s | 262.2 KiB | 00m00s [ 79/166] Installing libffi-0:3.4.6-5.f 100% | 44.6 MiB/s | 91.3 KiB | 00m00s [ 80/166] Installing libtasn1-0:4.19.0- 100% | 72.0 MiB/s | 221.1 KiB | 00m00s [ 81/166] Installing p11-kit-0:0.25.5-5 100% | 61.5 MiB/s | 2.8 MiB | 00m00s [ 82/166] Installing libunistring-0:1.1 100% | 144.0 MiB/s | 1.9 MiB | 00m00s [ 83/166] Installing libidn2-0:2.3.7-3. 100% | 55.6 MiB/s | 398.7 KiB | 00m00s [ 84/166] Installing libpsl-0:0.21.5-5. 100% | 65.1 MiB/s | 133.2 KiB | 00m00s [ 85/166] Installing p11-kit-trust-0:0. 100% | 17.2 MiB/s | 528.8 KiB | 00m00s [ 86/166] Installing zstd-0:1.5.6-3.fc4 100% | 57.1 MiB/s | 1.9 MiB | 00m00s [ 87/166] Installing tar-2:1.35-5.fc42. 100% | 71.1 MiB/s | 3.1 MiB | 00m00s [ 88/166] Installing libsemanage-0:3.8- 100% | 83.1 MiB/s | 425.7 KiB | 00m00s [ 89/166] Installing shadow-utils-2:4.1 100% | 68.2 MiB/s | 5.0 MiB | 00m00s [ 90/166] Installing zip-0:3.0-43.fc42. 100% | 29.1 MiB/s | 893.7 KiB | 00m00s [ 91/166] Installing gdbm-1:1.23-9.fc42 100% | 21.4 MiB/s | 612.7 KiB | 00m00s [ 92/166] Installing cyrus-sasl-lib-0:2 100% | 67.8 MiB/s | 2.9 MiB | 00m00s [ 93/166] Installing bzip2-0:1.0.8-20.f 100% | 6.6 MiB/s | 175.7 KiB | 00m00s [ 94/166] Installing libxml2-0:2.12.9-2 100% | 59.7 MiB/s | 2.3 MiB | 00m00s [ 95/166] Installing sqlite-libs-0:3.47 100% | 127.7 MiB/s | 1.9 MiB | 00m00s [ 96/166] Installing add-determinism-0: 100% | 65.1 MiB/s | 2.5 MiB | 00m00s [ 97/166] Installing build-reproducibil 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [ 98/166] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [ 99/166] Installing ed-0:1.21-2.fc42.p 100% | 4.8 MiB/s | 156.7 KiB | 00m00s [100/166] Installing patch-0:2.7.6-26.f 100% | 12.3 MiB/s | 327.9 KiB | 00m00s [101/166] Installing elfutils-default-y 100% | 510.7 KiB/s | 2.0 KiB | 00m00s [102/166] Installing elfutils-libs-0:0. 100% | 122.2 MiB/s | 876.0 KiB | 00m00s [103/166] Installing dbus-common-1:1.16 100% | 2.6 MiB/s | 13.6 KiB | 00m00s [104/166] Installing cpio-0:2.15-2.fc41 100% | 39.4 MiB/s | 1.2 MiB | 00m00s [105/166] Installing diffutils-0:3.10-9 100% | 46.4 MiB/s | 1.7 MiB | 00m00s [106/166] Installing librtas-0:2.0.6-3. 100% | 33.4 MiB/s | 307.5 KiB | 00m00s [107/166] Installing libgomp-0:15.0.1-0 100% | 125.2 MiB/s | 640.8 KiB | 00m00s [108/166] Installing jansson-0:2.14-2.f 100% | 77.4 MiB/s | 158.4 KiB | 00m00s [109/166] Installing libpkgconf-0:2.3.0 100% | 65.9 MiB/s | 135.0 KiB | 00m00s [110/166] Installing pkgconf-0:2.3.0-2. 100% | 5.1 MiB/s | 114.9 KiB | 00m00s [111/166] Installing pkgconf-pkg-config 100% | 84.4 KiB/s | 1.8 KiB | 00m00s [112/166] Installing keyutils-libs-0:1. 100% | 48.5 MiB/s | 99.4 KiB | 00m00s [113/166] Installing libverto-0:0.3.2-1 100% | 69.2 MiB/s | 70.9 KiB | 00m00s [114/166] Installing json-c-0:0.18-2.fc 100% | 68.3 MiB/s | 139.8 KiB | 00m00s [115/166] Installing libseccomp-0:2.5.5 100% | 100.0 MiB/s | 307.1 KiB | 00m00s [116/166] Installing expat-0:2.6.4-2.fc 100% | 9.0 MiB/s | 350.6 KiB | 00m00s [117/166] Installing dbus-broker-0:36-5 100% | 18.0 MiB/s | 552.3 KiB | 00m00s [118/166] Installing dbus-1:1.16.0-3.fc 100% | 0.0 B/s | 124.0 B | 00m00s [119/166] Installing libnghttp2-0:1.64. 100% | 97.2 MiB/s | 199.1 KiB | 00m00s [120/166] Installing xxhash-libs-0:0.8. 100% | 42.5 MiB/s | 87.0 KiB | 00m00s [121/166] Installing libbrotli-0:1.1.0- 100% | 119.0 MiB/s | 975.0 KiB | 00m00s [122/166] Installing libtool-ltdl-0:2.5 100% | 9.3 MiB/s | 95.0 KiB | 00m00s [123/166] Installing coreutils-common-0 100% | 146.8 MiB/s | 11.2 MiB | 00m00s [124/166] Installing openssl-libs-1:3.2 100% | 158.6 MiB/s | 7.8 MiB | 00m00s [125/166] Installing coreutils-0:9.6-1. 100% | 111.5 MiB/s | 9.5 MiB | 00m00s [126/166] Installing ca-certificates-0: 100% | 1.2 MiB/s | 2.4 MiB | 00m02s [127/166] Installing krb5-libs-0:1.21.3 100% | 123.7 MiB/s | 3.0 MiB | 00m00s [128/166] Installing libarchive-0:3.7.7 100% | 126.6 MiB/s | 1.3 MiB | 00m00s [129/166] Installing gzip-0:1.13-3.fc42 100% | 15.0 MiB/s | 430.2 KiB | 00m00s [130/166] Installing authselect-libs-0: 100% | 61.4 MiB/s | 880.4 KiB | 00m00s [131/166] Installing cracklib-0:2.9.11- 100% | 13.2 MiB/s | 433.0 KiB | 00m00s [132/166] Installing libpwquality-0:1.4 100% | 17.8 MiB/s | 620.7 KiB | 00m00s [133/166] Installing libtirpc-0:1.3.6-1 100% | 54.0 MiB/s | 276.4 KiB | 00m00s [134/166] Installing pam-0:1.7.0-4.fc42 100% | 64.8 MiB/s | 4.3 MiB | 00m00s [135/166] Installing util-linux-0:2.40. 100% | 81.3 MiB/s | 6.7 MiB | 00m00s [136/166] Installing systemd-pam-0:257. 100% | 101.5 MiB/s | 1.4 MiB | 00m00s [137/166] Installing systemd-0:257.2-17 100% | 56.6 MiB/s | 22.4 MiB | 00m00s >>> Running post-install scriptlet: systemd-0:257.2-17.fc42.ppc64le >>> Finished post-install scriptlet: systemd-0:257.2-17.fc42.ppc64le >>> Scriptlet output: >>> Creating group 'systemd-journal' with GID 190. >>> Creating group 'systemd-oom' with GID 999. >>> Creating user 'systemd-oom' (systemd Userspace OOM Killer) with UID 999 and >>> [138/166] Installing libssh-0:0.11.1-4. 100% | 99.8 MiB/s | 715.6 KiB | 00m00s [139/166] Installing rpm-sequoia-0:1.7. 100% | 140.2 MiB/s | 2.8 MiB | 00m00s [140/166] Installing rpm-libs-0:4.20.0- 100% | 121.0 MiB/s | 991.2 KiB | 00m00s [141/166] Installing rpm-build-libs-0:4 100% | 85.7 MiB/s | 263.3 KiB | 00m00s [142/166] Installing libevent-0:2.1.12- 100% | 134.4 MiB/s | 1.2 MiB | 00m00s [143/166] Installing openldap-0:2.6.9-3 100% | 109.0 MiB/s | 893.0 KiB | 00m00s [144/166] Installing libcurl-0:8.11.1-4 100% | 128.3 MiB/s | 1.0 MiB | 00m00s [145/166] Installing elfutils-debuginfo 100% | 5.7 MiB/s | 145.7 KiB | 00m00s [146/166] Installing elfutils-0:0.192-8 100% | 76.7 MiB/s | 3.5 MiB | 00m00s [147/166] Installing binutils-0:2.43.50 100% | 145.4 MiB/s | 31.3 MiB | 00m00s [148/166] Installing gdb-minimal-0:15.2 100% | 132.4 MiB/s | 15.4 MiB | 00m00s [149/166] Installing debugedit-0:5.1-4. 100% | 12.1 MiB/s | 310.8 KiB | 00m00s [150/166] Installing curl-0:8.11.1-4.fc 100% | 15.0 MiB/s | 521.1 KiB | 00m00s [151/166] Installing rpm-0:4.20.0-8.fc4 100% | 46.3 MiB/s | 2.7 MiB | 00m00s [152/166] Installing efi-srpm-macros-0: 100% | 40.1 MiB/s | 41.1 KiB | 00m00s [153/166] Installing tree-sitter-srpm-m 100% | 7.2 MiB/s | 7.4 KiB | 00m00s [154/166] Installing lua-srpm-macros-0: 100% | 1.9 MiB/s | 1.9 KiB | 00m00s [155/166] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [156/166] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [157/166] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [158/166] Installing fonts-srpm-macros- 100% | 27.8 MiB/s | 57.0 KiB | 00m00s [159/166] Installing python-srpm-macros 100% | 25.5 MiB/s | 52.2 KiB | 00m00s [160/166] Installing redhat-rpm-config- 100% | 37.8 MiB/s | 193.5 KiB | 00m00s [161/166] Installing rpm-build-0:4.20.0 100% | 17.3 MiB/s | 532.9 KiB | 00m00s [162/166] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [163/166] Installing authselect-0:1.5.0 100% | 6.9 MiB/s | 184.2 KiB | 00m00s [164/166] Installing which-0:2.23-1.fc4 100% | 5.3 MiB/s | 125.5 KiB | 00m00s [165/166] Installing info-0:7.2-3.fc42. 100% | 17.6 MiB/s | 485.8 KiB | 00m00s [166/166] Installing systemd-rpm-macros 100% | 3.9 KiB/s | 11.3 KiB | 00m03s Warning: skipped OpenPGP checks for 164 packages from repositories: copr_base, http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.5.0-2.fc42.ppc64le alternatives-1.31-3.fc42.ppc64le ansible-srpm-macros-1-17.1.fc42.noarch audit-libs-4.0.3-2.fc42.ppc64le authselect-1.5.0-9.fc42.ppc64le authselect-libs-1.5.0-9.fc42.ppc64le basesystem-11-22.fc42.noarch bash-5.2.37-1.fc42.ppc64le binutils-2.43.50-12.fc42.ppc64le build-reproducibility-srpm-macros-0.5.0-2.fc42.noarch bzip2-1.0.8-20.fc42.ppc64le bzip2-libs-1.0.8-20.fc42.ppc64le ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch coreutils-9.6-1.fc42.ppc64le coreutils-common-9.6-1.fc42.ppc64le cpio-2.15-2.fc41.ppc64le cracklib-2.9.11-7.fc42.ppc64le crypto-policies-20250124-1.git4d262e7.fc42.noarch curl-8.11.1-4.fc42.ppc64le cyrus-sasl-lib-2.1.28-30.fc42.ppc64le dbus-1.16.0-3.fc42.ppc64le dbus-broker-36-5.fc42.ppc64le dbus-common-1.16.0-3.fc42.noarch debugedit-5.1-4.fc42.ppc64le diffutils-3.10-9.fc42.ppc64le dwz-0.15-9.fc42.ppc64le ed-1.21-2.fc42.ppc64le efi-srpm-macros-6-2.fc42.noarch elfutils-0.192-8.fc42.ppc64le elfutils-debuginfod-client-0.192-8.fc42.ppc64le elfutils-default-yama-scope-0.192-8.fc42.noarch elfutils-libelf-0.192-8.fc42.ppc64le elfutils-libs-0.192-8.fc42.ppc64le expat-2.6.4-2.fc42.ppc64le fedora-gpg-keys-42-0.4.noarch fedora-release-42-0.16.noarch fedora-release-common-42-0.16.noarch fedora-release-identity-basic-42-0.16.noarch fedora-repos-42-0.4.noarch fedora-repos-rawhide-42-0.4.noarch file-5.46-1.fc42.ppc64le file-libs-5.46-1.fc42.ppc64le filesystem-3.18-36.fc42.ppc64le filesystem-srpm-macros-3.18-36.fc42.noarch findutils-4.10.0-5.fc42.ppc64le fonts-srpm-macros-2.0.5-21.fc42.noarch forge-srpm-macros-0.4.0-2.fc42.noarch fpc-srpm-macros-1.3-14.fc42.noarch gawk-5.3.1-1.fc42.ppc64le gdb-minimal-15.2-7.fc42.ppc64le gdbm-1.23-9.fc42.ppc64le gdbm-libs-1.23-9.fc42.ppc64le ghc-srpm-macros-1.9.2-2.fc42.noarch glibc-2.40.9000-35.fc42.ppc64le glibc-common-2.40.9000-35.fc42.ppc64le glibc-gconv-extra-2.40.9000-35.fc42.ppc64le glibc-minimal-langpack-2.40.9000-35.fc42.ppc64le gmp-6.3.0-2.fc41.ppc64le gnat-srpm-macros-6-7.fc42.noarch go-srpm-macros-3.6.0-6.fc42.noarch grep-3.11-10.fc42.ppc64le gzip-1.13-3.fc42.ppc64le info-7.2-3.fc42.ppc64le jansson-2.14-2.fc42.ppc64le json-c-0.18-2.fc42.ppc64le kernel-srpm-macros-1.0-25.fc42.noarch keyutils-libs-1.6.3-5.fc42.ppc64le krb5-libs-1.21.3-5.fc42.ppc64le libacl-2.3.2-3.fc42.ppc64le libarchive-3.7.7-2.fc42.ppc64le libattr-2.5.2-5.fc42.ppc64le libblkid-2.40.4-2.fc42.ppc64le libbrotli-1.1.0-6.fc42.ppc64le libcap-2.73-2.fc42.ppc64le libcap-ng-0.8.5-4.fc42.ppc64le libcom_err-1.47.2-3.fc42.ppc64le libcurl-8.11.1-4.fc42.ppc64le libeconf-0.7.5-2.fc42.ppc64le libevent-2.1.12-15.fc42.ppc64le libfdisk-2.40.4-2.fc42.ppc64le libffi-3.4.6-5.fc42.ppc64le libgcc-15.0.1-0.6.fc42.ppc64le libgomp-15.0.1-0.6.fc42.ppc64le libidn2-2.3.7-3.fc42.ppc64le libmount-2.40.4-2.fc42.ppc64le libnghttp2-1.64.0-3.fc42.ppc64le libpkgconf-2.3.0-2.fc42.ppc64le libpsl-0.21.5-5.fc42.ppc64le libpwquality-1.4.5-12.fc42.ppc64le librtas-2.0.6-3.fc42.ppc64le libseccomp-2.5.5-2.fc41.ppc64le libselinux-3.8-1.fc42.ppc64le libsemanage-3.8-1.fc42.ppc64le libsepol-3.8-1.fc42.ppc64le libsmartcols-2.40.4-2.fc42.ppc64le libssh-0.11.1-4.fc42.ppc64le libssh-config-0.11.1-4.fc42.noarch libstdc++-15.0.1-0.6.fc42.ppc64le libtasn1-4.19.0-11.fc42.ppc64le libtirpc-1.3.6-1.rc3.fc42.2.ppc64le libtool-ltdl-2.5.4-4.fc42.ppc64le libunistring-1.1-9.fc42.ppc64le libuuid-2.40.4-2.fc42.ppc64le libverto-0.3.2-10.fc42.ppc64le libxcrypt-4.4.38-4.fc42.ppc64le libxml2-2.12.9-2.fc42.ppc64le libzstd-1.5.6-3.fc42.ppc64le lua-libs-5.4.7-2.fc42.ppc64le lua-srpm-macros-1-15.fc42.noarch lz4-libs-1.10.0-2.fc42.ppc64le mpfr-4.2.1-6.fc42.ppc64le ncurses-base-6.5-5.20250125.fc42.noarch ncurses-libs-6.5-5.20250125.fc42.ppc64le ocaml-srpm-macros-10-4.fc42.noarch openblas-srpm-macros-2-19.fc42.noarch openldap-2.6.9-3.fc42.ppc64le openssl-libs-3.2.2-14.fc42.ppc64le p11-kit-0.25.5-5.fc42.ppc64le p11-kit-trust-0.25.5-5.fc42.ppc64le package-notes-srpm-macros-0.5-13.fc42.noarch pam-1.7.0-4.fc42.ppc64le pam-libs-1.7.0-4.fc42.ppc64le patch-2.7.6-26.fc42.ppc64le pcre2-10.44-1.fc42.2.ppc64le pcre2-syntax-10.44-1.fc42.2.noarch perl-srpm-macros-1-57.fc42.noarch pkgconf-2.3.0-2.fc42.ppc64le pkgconf-m4-2.3.0-2.fc42.noarch pkgconf-pkg-config-2.3.0-2.fc42.ppc64le popt-1.19-8.fc42.ppc64le publicsuffix-list-dafsa-20250116-1.fc42.noarch pyproject-srpm-macros-1.16.4-2.fc42.noarch python-srpm-macros-3.13-4.fc42.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.2-1.fc42.noarch readline-8.2-12.fc42.ppc64le redhat-rpm-config-342-2.fc42.noarch rpm-4.20.0-8.fc42.ppc64le rpm-build-4.20.0-8.fc42.ppc64le rpm-build-libs-4.20.0-8.fc42.ppc64le rpm-libs-4.20.0-8.fc42.ppc64le rpm-sequoia-1.7.0-4.fc42.ppc64le rust-srpm-macros-26.3-4.fc42.noarch sed-4.9-4.fc42.ppc64le setup-2.15.0-10.fc42.noarch shadow-utils-4.17.0-4.fc42.ppc64le sqlite-libs-3.47.2-2.fc42.ppc64le systemd-257.2-17.fc42.ppc64le systemd-libs-257.2-17.fc42.ppc64le systemd-pam-257.2-17.fc42.ppc64le systemd-rpm-macros-257.2-17.fc42.noarch tar-1.35-5.fc42.ppc64le tree-sitter-srpm-macros-0.1.0-8.fc42.noarch unzip-6.0-66.fc42.ppc64le util-linux-2.40.4-2.fc42.ppc64le util-linux-core-2.40.4-2.fc42.ppc64le which-2.23-1.fc42.ppc64le xxhash-libs-0.8.3-2.fc42.ppc64le xz-5.6.3-3.fc42.ppc64le xz-libs-5.6.3-3.fc42.ppc64le zig-srpm-macros-1-4.fc42.noarch zip-3.0-43.fc42.ppc64le zlib-ng-compat-2.2.3-2.fc42.ppc64le zstd-1.5.6-3.fc42.ppc64le Start: buildsrpm Start: rpmbuild -bs Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1738627200 Wrote: /builddir/build/SRPMS/pymol-3.1.0-3.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-ppc64le-1738674685.498307/root/var/log/dnf5.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-o7wyz67w/pymol/pymol.spec) Config(child) 0 minutes 44 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-3.1.0-3.fc42.src.rpm) Config(fedora-41-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-ppc64le-bootstrap-1738674685.498307/root. INFO: reusing tmpfs at /var/lib/mock/fedora-41-ppc64le-bootstrap-1738674685.498307/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/fedora-41-ppc64le-1738674685.498307/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-4.20.0-1.fc41.ppc64le rpm-sequoia-1.7.0-3.fc41.ppc64le dnf5-5.2.8.1-3.fc41.ppc64le dnf5-plugins-5.2.8.1-3.fc41.ppc64le Finish: chroot init Start: build phase for pymol-3.1.0-3.fc42.src.rpm Start: build setup for pymol-3.1.0-3.fc42.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1738627200 Wrote: /builddir/build/SRPMS/pymol-3.1.0-3.fc42.src.rpm Updating and loading repositories: fedora 100% | 134.9 KiB/s | 6.1 KiB | 00m00s updates 100% | 176.9 KiB/s | 7.1 KiB | 00m00s Copr repository 100% | 30.1 KiB/s | 1.5 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 55.5 KiB/s | 3.8 KiB | 00m00s Repositories loaded. 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB qt6-qtscxml ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.5 MiB qt6-qtsensors ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB qt6-qtserialbus ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB qt6-qtserialport ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 291.0 KiB qt6-qtshadertools ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.7 MiB qt6-qtspeech ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 499.9 KiB qt6-qtsvg ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB qt6-qttools ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB qt6-qttools-common noarch 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.5 KiB qt6-qttools-libs-designer ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.8 MiB qt6-qttools-libs-designercomponents ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.0 MiB qt6-qttools-libs-help ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 722.3 KiB qt6-qtwebchannel ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 566.5 KiB qt6-qtwebsockets ppc64le 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 363.4 KiB qt6-rpm-macros noarch 6.8.2-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 KiB rav1e-libs ppc64le 0.7.1-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB rhash ppc64le 1.4.5-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 394.6 KiB rsvg-pixbuf-loader ppc64le 2.59.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 466.5 KiB samba-client-libs ppc64le 2:4.21.3-6.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 23.7 MiB samba-common noarch 2:4.21.3-6.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 210.1 KiB samba-common-libs ppc64le 2:4.21.3-6.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 303.0 KiB sdl2-compat ppc64le 2.30.52-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 613.6 KiB shared-mime-info ppc64le 2.3-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.3 MiB shiboken6 ppc64le 6.8.1.1-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 104.3 KiB snappy ppc64le 1.2.1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82.7 KiB soxr ppc64le 0.1.3-18.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 270.2 KiB speex ppc64le 1.2.0-19.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 200.3 KiB spirv-tools-libs ppc64le 2024.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.6 MiB srt-libs ppc64le 1.5.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB svt-av1-libs ppc64le 2.1.0-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.7 MiB sysprof-capture-devel ppc64le 47.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 297.9 KiB systemd-devel ppc64le 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 610.5 KiB tslib ppc64le 1.22-11.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.6 MiB twolame-libs ppc64le 0.4.0-6.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 221.3 KiB tzdata noarch 2024b-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB unbound-libs ppc64le 1.22.0-11.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB unixODBC ppc64le 2.3.12-6.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 MiB vapoursynth-libs ppc64le 70-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 MiB vim-filesystem noarch 2:9.1.1000-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40.0 B vo-amrwbenc ppc64le 0.1.3-22.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 177.8 KiB vulkan-headers noarch 1.4.304.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28.2 MiB vulkan-loader ppc64le 1.4.304.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 736.3 KiB vulkan-loader-devel ppc64le 1.4.304.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 KiB xcb-util ppc64le 0.4.1-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 70.0 KiB xcb-util-cursor ppc64le 0.1.5-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 71.1 KiB xcb-util-image ppc64le 0.4.1-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69.8 KiB xcb-util-keysyms ppc64le 0.4.1-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 68.3 KiB xcb-util-renderutil ppc64le 0.3.10-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72.2 KiB xcb-util-wm ppc64le 0.4.2-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 136.6 KiB xkeyboard-config noarch 2.43-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.6 MiB xml-common noarch 0.6.3-66.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 78.4 KiB xorg-x11-proto-devel noarch 2024.1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB xprop ppc64le 1.2.8-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 78.5 KiB xvidcore ppc64le 1.3.7-13.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 744.4 KiB xz-devel ppc64le 1:5.6.3-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 255.6 KiB zeromq ppc64le 4.3.5-21.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB zimg ppc64le 3.0.5-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 341.9 KiB zlib-ng-compat-devel ppc64le 2.2.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 107.0 KiB zvbi ppc64le 0.2.43-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB Transaction Summary: Installing: 510 packages Total size of inbound packages is 430 MiB. Need to download 430 MiB. After this operation, 2 GiB extra will be used (install 2 GiB, remove 0 B). [ 1/510] catch2-devel-0:2.13.10-6.fc42 100% | 2.4 MiB/s | 196.9 KiB | 00m00s [ 2/510] desktop-file-utils-0:0.27-3.f 100% | 918.5 KiB/s | 76.2 KiB | 00m00s [ 3/510] freeglut-devel-0:3.6.0-4.fc42 100% | 7.3 MiB/s | 886.7 KiB | 00m00s [ 4/510] freetype-devel-0:2.13.3-2.fc4 100% | 22.6 MiB/s | 1.0 MiB | 00m00s [ 5/510] glew-devel-0:2.2.0-10.fc42.pp 100% | 8.8 MiB/s | 216.5 KiB | 00m00s [ 6/510] glm-devel-0:1.0.1-3.fc42.noar 100% | 8.7 MiB/s | 248.5 KiB | 00m00s [ 7/510] gcc-c++-0:15.0.1-0.6.fc42.ppc 100% | 86.2 MiB/s | 13.5 MiB | 00m00s [ 8/510] libappstream-glib-0:0.8.3-3.f 100% | 15.4 MiB/s | 408.8 KiB | 00m00s [ 9/510] libpng-devel-2:1.6.44-2.fc42. 100% | 12.5 MiB/s | 294.5 KiB | 00m00s [ 10/510] libxml2-devel-0:2.12.9-2.fc42 100% | 17.9 MiB/s | 494.8 KiB | 00m00s [ 11/510] mmtf-cpp-devel-0:1.1.0-7.fc42 100% | 1.6 MiB/s | 30.4 KiB | 00m00s [ 12/510] gcc-0:15.0.1-0.6.fc42.ppc64le 100% | 80.7 MiB/s | 34.2 MiB | 00m00s [ 13/510] msgpack-devel-0:3.1.0-18.fc42 100% | 2.1 MiB/s | 311.7 KiB | 00m00s [ 14/510] netcdf-devel-0:4.9.2-8.fc42.p 100% | 4.7 MiB/s | 90.9 KiB | 00m00s [ 15/510] pyproject-rpm-macros-0:1.16.4 100% | 2.4 MiB/s | 44.6 KiB | 00m00s [ 16/510] python3-devel-0:3.13.1-4.fc42 100% | 15.9 MiB/s | 358.1 KiB | 00m00s [ 17/510] mesa-libGL-devel-0:24.3.4-3.f 100% | 101.6 KiB/s | 38.0 KiB | 00m00s [ 18/510] python3-pyside6-devel-0:6.8.1 100% | 12.3 MiB/s | 264.2 KiB | 00m00s [ 19/510] python3-qt5-devel-0:5.15.11-3 100% | 17.9 MiB/s | 385.0 KiB | 00m00s [ 20/510] freeglut-0:3.6.0-4.fc42.ppc64 100% | 7.7 MiB/s | 157.7 KiB | 00m00s [ 21/510] freetype-0:2.13.3-2.fc42.ppc6 100% | 20.5 MiB/s | 482.2 KiB | 00m00s [ 22/510] python3-pillow-0:11.1.0-2.fc4 100% | 13.0 MiB/s | 1.0 MiB | 00m00s [ 23/510] libGLEW-0:2.2.0-10.fc42.ppc64 100% | 7.9 MiB/s | 162.5 KiB | 00m00s [ 24/510] libstdc++-devel-0:15.0.1-0.6. 100% | 52.8 MiB/s | 2.7 MiB | 00m00s [ 25/510] libpng-2:1.6.44-2.fc42.ppc64l 100% | 5.9 MiB/s | 139.5 KiB | 00m00s [ 26/510] cpp-0:15.0.1-0.6.fc42.ppc64le 100% | 87.5 MiB/s | 11.3 MiB | 00m00s [ 27/510] msgpack-0:3.1.0-18.fc42.ppc64 100% | 556.1 KiB/s | 31.7 KiB | 00m00s [ 28/510] netcdf-0:4.9.2-8.fc42.ppc64le 100% | 33.6 MiB/s | 893.9 KiB | 00m00s [ 29/510] python3-0:3.13.1-4.fc42.ppc64 100% | 1.5 MiB/s | 28.3 KiB | 00m00s [ 30/510] python3-qt5-0:5.15.11-3.fc42. 100% | 32.5 MiB/s | 1.1 MiB | 00m00s [ 31/510] python3-libs-0:3.13.1-4.fc42. 100% | 91.8 MiB/s | 8.9 MiB | 00m00s [ 32/510] hdf5-0:1.14.5-2.fc42.ppc64le 100% | 55.3 MiB/s | 2.0 MiB | 00m00s [ 33/510] mesa-libGL-0:24.3.4-3.fc41.pp 100% | 654.4 KiB/s | 181.3 KiB | 00m00s [ 34/510] python3-qt5-base-0:5.15.11-3. 100% | 54.8 MiB/s | 2.9 MiB | 00m00s [ 35/510] python-qt5-rpm-macros-0:5.15. 100% | 343.3 KiB/s | 8.9 KiB | 00m00s [ 36/510] qt5-qtbase-0:5.15.16-2.fc42.p 100% | 62.6 MiB/s | 3.8 MiB | 00m00s [ 37/510] qt5-qtbase-common-0:5.15.16-2 100% | 629.0 KiB/s | 12.0 KiB | 00m00s [ 38/510] libicu-0:76.1-4.fc42.ppc64le 100% | 68.2 MiB/s | 10.9 MiB | 00m00s [ 39/510] mesa-libglapi-0:24.3.4-3.fc41 100% | 167.1 KiB/s | 52.3 KiB | 00m00s [ 40/510] hdf5-devel-0:1.14.5-2.fc42.pp 100% | 48.0 MiB/s | 1.4 MiB | 00m00s [ 41/510] mesa-filesystem-0:24.3.4-3.fc 100% | 229.7 KiB/s | 20.7 KiB | 00m00s [ 42/510] gcc-gfortran-0:15.0.1-0.6.fc4 100% | 97.1 MiB/s | 12.9 MiB | 00m00s [ 43/510] qt5-qtxmlpatterns-0:5.15.16-2 100% | 35.9 MiB/s | 993.1 KiB | 00m00s [ 44/510] mesa-libgbm-0:24.3.4-3.fc41.p 100% | 115.6 KiB/s | 27.5 KiB | 00m00s [ 45/510] qt5-qtx11extras-0:5.15.16-2.f 100% | 1.5 MiB/s | 34.5 KiB | 00m00s [ 46/510] qt5-qtwebsockets-0:5.15.16-2. 100% | 4.5 MiB/s | 92.1 KiB | 00m00s [ 47/510] qt5-qtwebchannel-0:5.15.16-2. 100% | 5.3 MiB/s | 109.5 KiB | 00m00s [ 48/510] qt5-qtsvg-0:5.15.16-2.fc42.pp 100% | 9.2 MiB/s | 197.9 KiB | 00m00s [ 49/510] qt5-qtserialport-0:5.15.16-2. 100% | 3.5 MiB/s | 68.0 KiB | 00m00s [ 50/510] qt5-qtsensors-0:5.15.16-2.fc4 100% | 10.5 MiB/s | 235.9 KiB | 00m00s [ 51/510] qt5-qtmultimedia-0:5.15.16-2. 100% | 25.8 MiB/s | 871.9 KiB | 00m00s [ 52/510] qt5-qtlocation-0:5.15.16-3.fc 100% | 60.7 MiB/s | 3.4 MiB | 00m00s [ 53/510] qt5-qtconnectivity-0:5.15.16- 100% | 18.0 MiB/s | 516.3 KiB | 00m00s [ 54/510] qt5-qtdeclarative-0:5.15.16-2 100% | 50.7 MiB/s | 4.6 MiB | 00m00s [ 55/510] qt5-qtbase-devel-0:5.15.16-2. 100% | 54.8 MiB/s | 3.3 MiB | 00m00s [ 56/510] qt5-qtbase-gui-0:5.15.16-2.fc 100% | 64.6 MiB/s | 7.1 MiB | 00m00s [ 57/510] libgfortran-0:15.0.1-0.6.fc42 100% | 14.6 MiB/s | 657.6 KiB | 00m00s [ 58/510] libquadmath-0:15.0.1-0.6.fc42 100% | 10.5 MiB/s | 204.6 KiB | 00m00s [ 59/510] libquadmath-devel-0:15.0.1-0. 100% | 1.2 MiB/s | 26.7 KiB | 00m00s [ 60/510] python3-pytest-0:8.3.4-2.fc42 100% | 50.5 MiB/s | 2.0 MiB | 00m00s [ 61/510] alsa-lib-0:1.2.13-4.fc42.ppc6 100% | 20.5 MiB/s | 547.0 KiB | 00m00s [ 62/510] gstreamer1-0:1.24.11-2.fc42.p 100% | 41.4 MiB/s | 1.7 MiB | 00m00s [ 63/510] glib2-0:2.83.2-6.fc42.ppc64le 100% | 55.3 MiB/s | 3.2 MiB | 00m00s [ 64/510] gstreamer1-plugins-bad-free-l 100% | 36.0 MiB/s | 957.5 KiB | 00m00s 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KiB/s | 26.6 KiB | 00m00s [398/510] libtommath-0:1.3.1~rc1-5.fc42 100% | 3.0 MiB/s | 76.4 KiB | 00m00s [399/510] libgcrypt-0:1.11.0-5.fc42.ppc 100% | 21.4 MiB/s | 657.9 KiB | 00m00s [400/510] libvdpau-0:1.5-9.fc42.ppc64le 100% | 736.2 KiB/s | 16.9 KiB | 00m00s [401/510] game-music-emu-0:0.6.3-17.fc4 100% | 6.8 MiB/s | 166.9 KiB | 00m00s [402/510] libchromaprint-0:1.5.1-24.fc4 100% | 2.1 MiB/s | 46.2 KiB | 00m00s [403/510] libbluray-0:1.3.4-9.fc42.ppc6 100% | 7.2 MiB/s | 191.8 KiB | 00m00s [404/510] libdvdnav-0:6.1.1-10.fc42.ppc 100% | 2.9 MiB/s | 58.8 KiB | 00m00s [405/510] libdvdread-0:6.1.3-9.fc42.ppc 100% | 3.8 MiB/s | 76.9 KiB | 00m00s [406/510] libmodplug-1:0.8.9.0-27.fc42. 100% | 8.3 MiB/s | 204.6 KiB | 00m00s [407/510] libopenmpt-0:0.7.13-3.fc42.pp 100% | 24.2 MiB/s | 769.1 KiB | 00m00s [408/510] librabbitmq-0:0.15.0-2.fc42.p 100% | 2.2 MiB/s | 48.7 KiB | 00m00s [409/510] librist-0:0.2.7-8.fc42.ppc64l 100% | 3.8 MiB/s | 85.3 KiB | 00m00s [410/510] libsmbclient-2:4.21.3-6.fc42. 100% | 4.5 MiB/s | 87.8 KiB | 00m00s [411/510] libldb-2:4.21.3-6.fc42.ppc64l 100% | 10.1 MiB/s | 216.7 KiB | 00m00s [412/510] libwbclient-2:4.21.3-6.fc42.p 100% | 2.9 MiB/s | 54.1 KiB | 00m00s [413/510] samba-common-libs-2:4.21.3-6. 100% | 5.5 MiB/s | 118.4 KiB | 00m00s [414/510] samba-common-2:4.21.3-6.fc42. 100% | 7.2 MiB/s | 177.7 KiB | 00m00s [415/510] srt-libs-0:1.5.4-2.fc42.ppc64 100% | 12.1 MiB/s | 397.5 KiB | 00m00s [416/510] vapoursynth-libs-0:70-1.fc42. 100% | 11.8 MiB/s | 436.1 KiB | 00m00s [417/510] zeromq-0:4.3.5-21.fc42.ppc64l 100% | 17.0 MiB/s | 469.6 KiB | 00m00s [418/510] samba-client-libs-2:4.21.3-6. 100% | 54.0 MiB/s | 5.9 MiB | 00m00s [419/510] openpgm-0:5.3.128-4.fc42.ppc6 100% | 3.8 MiB/s | 188.3 KiB | 00m00s [420/510] aribb24-0:1.0.3^20160216git5e 100% | 1.0 MiB/s | 41.4 KiB | 00m00s [421/510] fdk-aac-free-0:2.0.0-15.fc42. 100% | 12.1 MiB/s | 371.2 KiB | 00m00s [422/510] codec2-0:1.2.0-6.fc42.ppc64le 100% | 18.5 MiB/s | 682.4 KiB | 00m00s [423/510] ilbc-0:3.0.4-13.fc42.ppc64le 100% | 2.5 MiB/s | 59.6 KiB | 00m00s [424/510] libaribcaption-0:1.1.1-2.fc42 100% | 3.7 MiB/s | 114.3 KiB | 00m00s [425/510] libaom-0:3.9.0-5.fc42.ppc64le 100% | 31.0 MiB/s | 1.4 MiB | 00m00s [426/510] libdav1d-0:1.5.1-1.fc42.ppc64 100% | 11.4 MiB/s | 468.3 KiB | 00m00s [427/510] cairo-gobject-0:1.18.2-3.fc42 100% | 926.7 KiB/s | 17.6 KiB | 00m00s [428/510] rsvg-pixbuf-loader-0:2.59.2-2 100% | 9.3 MiB/s | 210.3 KiB | 00m00s [429/510] librsvg2-0:2.59.2-2.fc42.ppc6 100% | 35.1 MiB/s | 1.8 MiB | 00m00s [430/510] libvpx-0:1.15.0-2.fc42.ppc64l 100% | 36.2 MiB/s | 1.4 MiB | 00m00s [431/510] noopenh264-0:2.5.0-2.fc42.ppc 100% | 685.2 KiB/s | 21.9 KiB | 00m00s [432/510] opencore-amr-0:0.1.6-8.fc42.p 100% | 7.7 MiB/s | 189.1 KiB | 00m00s [433/510] speex-0:1.2.0-19.fc42.ppc64le 100% | 3.8 MiB/s | 81.7 KiB | 00m00s [434/510] rav1e-libs-0:0.7.1-5.fc42.ppc 100% | 26.6 MiB/s | 817.6 KiB | 00m00s [435/510] svt-av1-libs-0:2.1.0-5.fc42.p 100% | 32.0 MiB/s | 1.2 MiB | 00m00s [436/510] twolame-libs-0:0.4.0-6.fc42.p 100% | 3.0 MiB/s | 74.4 KiB | 00m00s [437/510] vo-amrwbenc-0:0.1.3-22.fc42.p 100% | 3.2 MiB/s | 89.0 KiB | 00m00s [438/510] xvidcore-0:1.3.7-13.fc42.ppc6 100% | 10.5 MiB/s | 257.7 KiB | 00m00s [439/510] zvbi-0:0.2.43-2.fc42.ppc64le 100% | 16.9 MiB/s | 467.6 KiB | 00m00s [440/510] gssdp-0:1.6.3-5.fc42.ppc64le 100% | 2.6 MiB/s | 60.6 KiB | 00m00s [441/510] gupnp-0:1.6.8-1.fc42.ppc64le 100% | 4.6 MiB/s | 116.5 KiB | 00m00s [442/510] libsoup3-0:3.6.4-2.fc42.ppc64 100% | 15.8 MiB/s | 404.7 KiB | 00m00s [443/510] gmp-c++-1:6.3.0-2.fc41.ppc64l 100% | 941.5 KiB/s | 18.8 KiB | 00m00s [444/510] libxcrypt-devel-0:4.4.38-4.fc 100% | 1.4 MiB/s | 29.2 KiB | 00m00s [445/510] systemd-devel-0:257.2-17.fc42 100% | 22.2 MiB/s | 546.0 KiB | 00m00s [446/510] highway-0:1.2.0-5.fc42.ppc64l 100% | 6.7 MiB/s | 171.2 KiB | 00m00s [447/510] poly2tri-0:0.0^20130501hg2624 100% | 1.4 MiB/s | 31.3 KiB | 00m00s [448/510] pugixml-0:1.14-2.fc42.ppc64le 100% | 5.1 MiB/s | 113.9 KiB | 00m00s [449/510] lpcnetfreedv-0:0.5-8.fc42.ppc 100% | 52.8 MiB/s | 7.3 MiB | 00m00s [450/510] libsodium-0:1.0.20-4.fc42.ppc 100% | 2.2 MiB/s | 146.5 KiB | 00m00s [451/510] zimg-0:3.0.5-3.fc41.ppc64le 100% | 5.2 MiB/s | 107.1 KiB | 00m00s [452/510] sdl2-compat-0:2.30.52-1.fc42. 100% | 5.8 MiB/s | 136.7 KiB | 00m00s [453/510] libtalloc-0:2.4.2-7.fc42.ppc6 100% | 1.3 MiB/s | 32.3 KiB | 00m00s [454/510] SDL3-0:3.2.2-1.fc42.ppc64le 100% | 27.2 MiB/s | 1.1 MiB | 00m00s [455/510] libtdb-0:1.4.12-5.fc42.ppc64l 100% | 2.4 MiB/s | 59.6 KiB | 00m00s [456/510] libtevent-0:0.16.1-7.fc42.ppc 100% | 2.7 MiB/s | 52.9 KiB | 00m00s [457/510] perl-Term-ANSIColor-0:5.01-51 100% | 2.7 MiB/s | 47.7 KiB | 00m00s [458/510] perl-Term-Cap-0:1.18-512.fc42 100% | 1.1 MiB/s | 22.2 KiB | 00m00s [459/510] ncurses-0:6.5-5.20250125.fc42 100% | 17.5 MiB/s | 429.1 KiB | 00m00s [460/510] perl-Pod-Escapes-1:1.07-512.f 100% | 1.1 MiB/s | 19.8 KiB | 00m00s [461/510] perl-Text-Tabs+Wrap-0:2024.00 100% | 1.3 MiB/s | 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755.2 KiB/s | 14.3 KiB | 00m00s [488/510] libcloudproviders-0:0.3.5-6.f 100% | 2.4 MiB/s | 47.1 KiB | 00m00s [489/510] libepoxy-0:1.5.10-9.fc42.ppc6 100% | 10.5 MiB/s | 235.7 KiB | 00m00s [490/510] libtracker-sparql-0:3.7.3-5.f 100% | 17.1 MiB/s | 403.0 KiB | 00m00s [491/510] avahi-glib-0:0.9~rc2-2.fc42.p 100% | 761.1 KiB/s | 15.2 KiB | 00m00s [492/510] libgusb-0:0.4.9-3.fc42.ppc64l 100% | 3.2 MiB/s | 65.2 KiB | 00m00s [493/510] libXtst-0:1.2.5-2.fc42.ppc64l 100% | 1.1 MiB/s | 22.0 KiB | 00m00s [494/510] xprop-0:1.2.8-3.fc42.ppc64le 100% | 1.7 MiB/s | 38.3 KiB | 00m00s [495/510] perl-Data-Dumper-0:2.189-513. 100% | 2.9 MiB/s | 58.5 KiB | 00m00s [496/510] perl-MIME-Base32-0:1.303-23.f 100% | 1.2 MiB/s | 20.5 KiB | 00m00s [497/510] adwaita-icon-theme-legacy-0:4 100% | 37.9 MiB/s | 2.2 MiB | 00m00s [498/510] perl-libnet-0:3.15-513.fc42.n 100% | 3.3 MiB/s | 122.9 KiB | 00m00s [499/510] perl-B-0:1.89-515.fc42.ppc64l 100% | 4.9 MiB/s | 179.9 KiB | 00m00s [500/510] libusb1-0:1.0.27-8.fc42.ppc64 100% | 3.8 MiB/s | 82.7 KiB | 00m00s [501/510] perl-FileHandle-0:2.05-515.fc 100% | 911.6 KiB/s | 15.5 KiB | 00m00s [502/510] perl-Digest-MD5-0:2.59-6.fc42 100% | 1.7 MiB/s | 36.1 KiB | 00m00s [503/510] perl-Digest-0:1.20-512.fc42.n 100% | 1.4 MiB/s | 24.9 KiB | 00m00s [504/510] OpenCL-ICD-Loader-0:3.0.6-2.2 100% | 1.5 MiB/s | 30.9 KiB | 00m00s [505/510] hdf-libs-0:4.3.0-3.fc42.ppc64 100% | 13.0 MiB/s | 319.3 KiB | 00m00s [506/510] gcc-plugin-annobin-0:15.0.1-0 100% | 2.2 MiB/s | 40.9 KiB | 00m00s [507/510] cmake-rpm-macros-0:3.31.5-1.f 100% | 946.2 KiB/s | 17.0 KiB | 00m00s [508/510] python3-rpm-generators-0:14-1 100% | 1.7 MiB/s | 29.2 KiB | 00m00s [509/510] annobin-docs-0:12.88-1.fc42.n 100% | 4.5 MiB/s | 91.7 KiB | 00m00s [510/510] annobin-plugin-gcc-0:12.88-1. 100% | 26.7 MiB/s | 983.9 KiB | 00m00s -------------------------------------------------------------------------------- [510/510] Total 100% | 57.7 MiB/s | 429.5 MiB | 00m07s Running transaction Importing OpenPGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. [ 1/512] Verify package files 100% | 111.0 B/s | 510.0 B | 00m05s [ 2/512] Prepare transaction 100% | 748.0 B/s | 510.0 B | 00m01s [ 3/512] Installing cmake-filesystem-0 100% | 2.5 MiB/s | 7.6 KiB | 00m00s [ 4/512] Installing dbus-libs-1:1.16.0 100% | 113.0 MiB/s | 462.9 KiB | 00m00s [ 5/512] Installing libjpeg-turbo-0:3. 100% | 141.3 MiB/s | 868.4 KiB | 00m00s [ 6/512] Installing libpng-2:1.6.44-2. 100% | 109.0 MiB/s | 334.9 KiB | 00m00s [ 7/512] Installing zlib-ng-compat-dev 100% | 53.0 MiB/s | 108.5 KiB | 00m00s [ 8/512] Installing libX11-xcb-0:1.8.1 100% | 65.9 MiB/s | 67.4 KiB | 00m00s [ 9/512] Installing libwayland-client- 100% | 69.4 MiB/s | 71.1 KiB | 00m00s [ 10/512] Installing libicu-0:76.1-4.fc 100% | 159.7 MiB/s | 37.8 MiB | 00m00s [ 11/512] Installing avahi-libs-0:0.9~r 100% | 96.4 MiB/s | 296.2 KiB | 00m00s [ 12/512] Installing libogg-2:1.3.5-11. 100% | 76.7 MiB/s | 78.6 KiB | 00m00s [ 13/512] Installing qt6-qttools-common 100% | 0.0 B/s | 7.9 KiB | 00m00s [ 14/512] 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KiB | 00m00s [230/512] Installing perl-Pod-Perldoc-0 100% | 5.9 MiB/s | 169.2 KiB | 00m00s [231/512] Installing perl-Fcntl-0:1.18- 100% | 45.7 MiB/s | 93.7 KiB | 00m00s [232/512] Installing perl-Text-ParseWor 100% | 14.2 MiB/s | 14.6 KiB | 00m00s [233/512] Installing perl-base-0:2.27-5 100% | 12.6 MiB/s | 12.9 KiB | 00m00s [234/512] Installing perl-mro-0:1.29-51 100% | 40.2 MiB/s | 82.3 KiB | 00m00s [235/512] Installing perl-IO-0:1.55-515 100% | 47.6 MiB/s | 194.9 KiB | 00m00s [236/512] Installing perl-overloading-0 100% | 5.4 MiB/s | 5.5 KiB | 00m00s [237/512] Installing perl-Pod-Usage-4:2 100% | 3.5 MiB/s | 86.3 KiB | 00m00s [238/512] Installing perl-Errno-0:1.38- 100% | 8.5 MiB/s | 8.7 KiB | 00m00s [239/512] Installing perl-Scalar-List-U 100% | 38.1 MiB/s | 156.2 KiB | 00m00s [240/512] Installing perl-constant-0:1. 100% | 26.7 MiB/s | 27.4 KiB | 00m00s [241/512] Installing perl-vars-0:1.05-5 100% | 4.2 MiB/s | 4.3 KiB | 00m00s [242/512] Installing perl-Getopt-Std-0: 100% | 11.5 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perl-interpreter-4 100% | 6.9 MiB/s | 175.7 KiB | 00m00s [256/512] Installing perl-English-0:1.1 100% | 6.5 MiB/s | 6.6 KiB | 00m00s [257/512] Installing perl-File-Find-0:1 100% | 41.5 MiB/s | 42.5 KiB | 00m00s [258/512] Installing libxslt-0:1.1.42-4 100% | 22.8 MiB/s | 677.7 KiB | 00m00s [259/512] Installing qt6-filesystem-0:6 100% | 1.7 MiB/s | 3.5 KiB | 00m00s [260/512] Installing unixODBC-0:2.3.12- 100% | 36.1 MiB/s | 1.4 MiB | 00m00s [261/512] Installing libpq-0:16.4-2.fc4 100% | 118.2 MiB/s | 1.1 MiB | 00m00s [262/512] Installing protobuf-c-0:1.5.0 100% | 101.3 MiB/s | 207.4 KiB | 00m00s [263/512] Installing hiredis-0:1.2.0-6. 100% | 99.3 MiB/s | 203.3 KiB | 00m00s [264/512] Installing p11-kit-devel-0:0. 100% | 78.5 MiB/s | 562.7 KiB | 00m00s [265/512] Installing libtasn1-tools-0:4 100% | 8.1 MiB/s | 206.7 KiB | 00m00s [266/512] Installing libtasn1-devel-0:4 100% | 20.3 MiB/s | 83.1 KiB | 00m00s [267/512] Installing lm_sensors-libs-0: 100% | 46.3 MiB/s | 94.8 KiB | 00m00s 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avahi-0:0.9~rc2-2.fc42.ppc64le >>> Finished post-install scriptlet: avahi-0:0.9~rc2-2.fc42.ppc64le >>> Scriptlet output: >>> Created symlink '/etc/systemd/system/sockets.target.wants/avahi-daemon.socke >>> Created symlink '/etc/systemd/system/dbus-org.freedesktop.Avahi.service' → >>> Created symlink '/etc/systemd/system/multi-user.target.wants/avahi-daemon.se >>> [280/512] Installing rhash-0:1.4.5-2.fc 100% | 13.9 MiB/s | 399.9 KiB | 00m00s [281/512] Installing libuv-1:1.50.0-1.f 100% | 108.8 MiB/s | 668.8 KiB | 00m00s [282/512] Installing vim-filesystem-2:9 100% | 2.3 MiB/s | 4.7 KiB | 00m00s [283/512] Installing google-noto-fonts- 100% | 18.1 MiB/s | 18.5 KiB | 00m00s [284/512] Installing google-noto-sans-v 100% | 139.1 MiB/s | 1.4 MiB | 00m00s [285/512] Installing default-fonts-core 100% | 5.9 MiB/s | 18.2 KiB | 00m00s [286/512] Installing fontconfig-0:2.16. 100% | 1.3 MiB/s | 1.4 MiB | 00m01s [287/512] Installing libbluray-0:1.3.4- 100% | 96.7 MiB/s | 495.2 KiB | 00m00s [288/512] Installing libaribcaption-0:1 100% | 89.0 MiB/s | 273.3 KiB | 00m00s [289/512] Installing gettext-envsubst-0 100% | 4.4 MiB/s | 108.1 KiB | 00m00s [290/512] Installing gettext-runtime-0: 100% | 15.8 MiB/s | 517.3 KiB | 00m00s [291/512] Installing gettext-0:0.23.1-2 100% | 92.5 MiB/s | 5.9 MiB | 00m00s [292/512] Installing bzip2-devel-0:1.0. 100% | 151.7 MiB/s | 310.7 KiB | 00m00s [293/512] Installing libubsan-0:15.0.1- 100% | 130.8 MiB/s | 669.5 KiB | 00m00s [294/512] Installing libatomic-0:15.0.1 100% | 67.4 MiB/s | 69.0 KiB | 00m00s [295/512] Installing libasan-0:15.0.1-0 100% | 161.8 MiB/s | 2.1 MiB | 00m00s [296/512] Installing gcc-0:15.0.1-0.6.f 100% | 162.2 MiB/s | 96.8 MiB | 00m01s [297/512] Installing libquadmath-devel- 100% | 22.9 MiB/s | 23.4 KiB | 00m00s [298/512] Installing gcc-gfortran-0:15. 100% | 144.6 MiB/s | 37.3 MiB | 00m00s [299/512] Installing hdf5-devel-0:1.14. 100% | 73.9 MiB/s | 3.3 MiB | 00m00s [300/512] Installing sysprof-capture-de 100% | 97.9 MiB/s | 300.8 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00m00s [339/512] Installing netcdf-0:4.9.2-8.f 100% | 75.6 MiB/s | 3.5 MiB | 00m00s [340/512] Installing fmt-0:11.1.2-2.fc4 100% | 105.3 MiB/s | 323.5 KiB | 00m00s [341/512] Installing openal-soft-0:1.24 100% | 50.8 MiB/s | 1.8 MiB | 00m00s [342/512] Installing libasyncns-0:0.8-3 100% | 49.0 MiB/s | 100.3 KiB | 00m00s [343/512] Installing pulseaudio-libs-0: 100% | 120.9 MiB/s | 3.7 MiB | 00m00s [344/512] Installing tzdata-0:2024b-2.f 100% | 20.3 MiB/s | 1.9 MiB | 00m00s [345/512] Installing python-pip-wheel-0 100% | 207.4 MiB/s | 1.2 MiB | 00m00s [346/512] Installing mpdecimal-0:2.5.1- 100% | 32.5 MiB/s | 266.0 KiB | 00m00s [347/512] Installing python3-libs-0:3.1 100% | 131.1 MiB/s | 43.4 MiB | 00m00s [348/512] Installing python3-0:3.13.1-4 100% | 3.3 MiB/s | 85.3 KiB | 00m00s [349/512] Installing gstreamer1-0:1.24. 100% | 88.0 MiB/s | 6.6 MiB | 00m00s [350/512] Installing python3-packaging- 100% | 69.3 MiB/s | 568.0 KiB | 00m00s [351/512] Installing python3-shiboken6- 100% | 92.0 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Finish: build setup for pymol-3.1.0-3.fc42.src.rpm Start: rpmbuild pymol-3.1.0-3.fc42.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1738627200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.8FSlkk + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-build + test -d /builddir/build/BUILD/pymol-3.1.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/pymol-3.1.0-build + /usr/bin/rm -rf /builddir/build/BUILD/pymol-3.1.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/pymol-3.1.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.yduY1F + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-build + cd /builddir/build/BUILD/pymol-3.1.0-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 + /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 + 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.0KXZlX + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + 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-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-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement not satisfied: numpy>=1.26.4,<3 Handling setuptools>=69.2.0 from build-system.requires Requirement not satisfied: setuptools>=69.2.0 Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-3.fc42.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 242.8 KiB/s | 6.1 KiB | 00m00s updates 100% | 228.3 KiB/s | 7.1 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 70.9 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 43.9 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "catch2-devel-2.13.10-6.fc42.ppc64le" is already installed. Package "desktop-file-utils-0.27-3.fc42.ppc64le" is already installed. Package "freeglut-devel-3.6.0-4.fc42.ppc64le" is already installed. Package "freetype-devel-2.13.3-2.fc42.ppc64le" is already installed. Package "gcc-15.0.1-0.6.fc42.ppc64le" is already installed. Package "gcc-c++-15.0.1-0.6.fc42.ppc64le" is already installed. Package "glew-devel-2.2.0-10.fc42.ppc64le" is already installed. Package "glm-devel-1.0.1-3.fc42.noarch" is already installed. Package "mesa-libGL-devel-24.3.4-3.fc41.ppc64le" is already installed. Package "libappstream-glib-0.8.3-3.fc42.ppc64le" is already installed. Package "libpng-devel-2:1.6.44-2.fc42.ppc64le" is already installed. Package "libxml2-devel-2.12.9-2.fc42.ppc64le" is already installed. Package "mmtf-cpp-devel-1.1.0-7.fc42.ppc64le" is already installed. Package "msgpack-devel-3.1.0-18.fc42.ppc64le" is already installed. Package "netcdf-devel-4.9.2-8.fc42.ppc64le" is already installed. Package "pyproject-rpm-macros-1.16.4-2.fc42.noarch" is already installed. Package "python3-devel-3.13.1-4.fc42.ppc64le" is already installed. Package "python3-pillow-11.1.0-2.fc42.ppc64le" is already installed. Package "python3-pyside6-devel-6.8.1.1-3.fc42.ppc64le" is already installed. Package "python3-pytest-8.3.4-2.fc42.noarch" is already installed. Package "python3-qt5-devel-5.15.11-3.fc42.ppc64le" is already installed. Package "python3-packaging-24.2-3.fc42.noarch" is already installed. Package Arch Version Repository Size Installing: python3-numpy ppc64le 1:2.2.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37.0 MiB python3-pip noarch 24.3.1-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11.3 MiB python3-setuptools noarch 74.1.3-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.4 MiB Installing dependencies: flexiblas ppc64le 3.4.4-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 48.5 KiB flexiblas-netlib ppc64le 3.4.4-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11.9 MiB flexiblas-openblas-openmp ppc64le 3.4.4-7.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 66.9 KiB openblas ppc64le 0.3.29-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 111.7 KiB openblas-openmp ppc64le 0.3.29-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 23.2 MiB python3-numpy-f2py ppc64le 1:2.2.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB Transaction Summary: Installing: 9 packages Total size of inbound packages is 20 MiB. Need to download 20 MiB. After this operation, 94 MiB extra will be used (install 94 MiB, remove 0 B). [1/9] python3-setuptools-0:74.1.3-5.fc4 100% | 12.1 MiB/s | 1.8 MiB | 00m00s [2/9] python3-pip-0:24.3.1-2.fc42.noarc 100% | 15.1 MiB/s | 2.5 MiB | 00m00s [3/9] python3-numpy-1:2.2.2-2.fc42.ppc6 100% | 31.6 MiB/s | 7.0 MiB | 00m00s [4/9] python3-numpy-f2py-1:2.2.2-2.fc42 100% | 7.6 MiB/s | 449.3 KiB | 00m00s [5/9] flexiblas-netlib-0:3.4.4-7.fc42.p 100% | 32.7 MiB/s | 2.9 MiB | 00m00s [6/9] flexiblas-0:3.4.4-7.fc42.ppc64le 100% | 748.2 KiB/s | 25.4 KiB | 00m00s [7/9] flexiblas-openblas-openmp-0:3.4.4 100% | 559.5 KiB/s | 16.8 KiB | 00m00s [8/9] openblas-0:0.3.29-1.fc42.ppc64le 100% | 1.8 MiB/s | 42.2 KiB | 00m00s [9/9] openblas-openmp-0:0.3.29-1.fc42.p 100% | 65.2 MiB/s | 5.0 MiB | 00m00s -------------------------------------------------------------------------------- [9/9] Total 100% | 61.7 MiB/s | 19.8 MiB | 00m00s Running transaction [ 1/11] Verify package files 100% | 45.0 B/s | 9.0 B | 00m00s [ 2/11] Prepare transaction 100% | 52.0 B/s | 9.0 B | 00m00s [ 3/11] Installing openblas-0:0.3.29-1. 100% | 36.9 MiB/s | 113.5 KiB | 00m00s [ 4/11] Installing openblas-openmp-0:0. 100% | 172.8 MiB/s | 23.2 MiB | 00m00s [ 5/11] Installing flexiblas-0:3.4.4-7. 100% | 48.5 MiB/s | 49.7 KiB | 00m00s [ 6/11] Installing flexiblas-openblas-o 100% | 33.1 MiB/s | 67.7 KiB | 00m00s [ 7/11] Installing flexiblas-netlib-0:3 100% | 120.1 MiB/s | 11.9 MiB | 00m00s [ 8/11] Installing python3-numpy-f2py-1 100% | 35.7 MiB/s | 2.1 MiB | 00m00s [ 9/11] Installing python3-numpy-1:2.2. 100% | 123.4 MiB/s | 37.3 MiB | 00m00s [10/11] Installing python3-setuptools-0 100% | 79.3 MiB/s | 8.6 MiB | 00m00s [11/11] Installing python3-pip-0:24.3.1 100% | 42.7 MiB/s | 11.6 MiB | 00m00s Warning: skipped OpenPGP checks for 9 packages from repository: http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch Complete! Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1738627200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.1wcqU9 + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + 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-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-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.2) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 74.1.3) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.2) 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-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-3.fc42.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: updates 100% | 160.8 KiB/s | 7.1 KiB | 00m00s Copr repository 100% | 27.4 KiB/s | 1.5 KiB | 00m00s fedora 100% | 224.8 KiB/s | 6.1 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 59.8 KiB/s | 3.8 KiB | 00m00s Repositories loaded. Package "catch2-devel-2.13.10-6.fc42.ppc64le" is already installed. Package "desktop-file-utils-0.27-3.fc42.ppc64le" is already installed. Package "freeglut-devel-3.6.0-4.fc42.ppc64le" is already installed. Package "freetype-devel-2.13.3-2.fc42.ppc64le" is already installed. Package "gcc-15.0.1-0.6.fc42.ppc64le" is already installed. Package "gcc-c++-15.0.1-0.6.fc42.ppc64le" is already installed. Package "glew-devel-2.2.0-10.fc42.ppc64le" is already installed. Package "glm-devel-1.0.1-3.fc42.noarch" is already installed. Package "mesa-libGL-devel-24.3.4-3.fc41.ppc64le" is already installed. Package "libappstream-glib-0.8.3-3.fc42.ppc64le" is already installed. Package "libpng-devel-2:1.6.44-2.fc42.ppc64le" is already installed. Package "libxml2-devel-2.12.9-2.fc42.ppc64le" is already installed. Package "mmtf-cpp-devel-1.1.0-7.fc42.ppc64le" is already installed. Package "msgpack-devel-3.1.0-18.fc42.ppc64le" is already installed. Package "netcdf-devel-4.9.2-8.fc42.ppc64le" is already installed. Package "pyproject-rpm-macros-1.16.4-2.fc42.noarch" is already installed. Package "python3-devel-3.13.1-4.fc42.ppc64le" is already installed. Package "python3-pillow-11.1.0-2.fc42.ppc64le" is already installed. Package "python3-pyside6-devel-6.8.1.1-3.fc42.ppc64le" is already installed. Package "python3-pytest-8.3.4-2.fc42.noarch" is already installed. Package "python3-qt5-devel-5.15.11-3.fc42.ppc64le" is already installed. Package "python3-packaging-24.2-3.fc42.noarch" is already installed. Package "python3-pip-24.3.1-2.fc42.noarch" is already installed. Package "python3-setuptools-74.1.3-5.fc42.noarch" is already installed. Nothing to do. Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1738627200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.RoRbbQ + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + 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-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-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.2) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 74.1.3) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.2) 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-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.QOIkRp + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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-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-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + 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-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir Processing /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0 -DTARGET_NAME=_cmd -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-ppc64le-cpython-313/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/python3.13/site-packages/numpy/_core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.13;/usr/include/python3.13; -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-313-powerpc64le-linux-gnu.so -- The C compiler identification is GNU 15.0.1 -- The CXX compiler identification is GNU 15.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.8s) -- Generating done (0.1s) -- Build files have been written to: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd cmake --build . --config Release -j5 /usr/bin/cmake -S/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd/CMakeFiles/_cmd.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' [ 1%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c.o [ 1%] Building CXX object CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o [ 1%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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/PlugIOManagerInit.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c /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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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/abinitplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp /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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o -MF CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp [ 1%] Building CXX object CMakeFiles/_cmd.dir/build/generated/ShaderText.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/build/generated/ShaderText.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerInitAll’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerFreeAll’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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; | ^~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘abinit_header’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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() { | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function ‘open_binpos_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘open_car_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: /builddir/build/BUILD/pymol-3.1.0-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:970, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: In function ‘*__sprintfieee128’, inlined from ‘read_car_structure_line’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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_chkieee128’ 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 ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:42: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ^~~~~~~~~~~~~~~ [ 5%] Building C object 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_timestep’: /builddir/build/BUILD/pymol-3.1.0-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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function ‘read_dcdstep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_structure’: /builddir/build/BUILD/pymol-3.1.0-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)); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ^~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘void eatline(FILE*)’: /builddir/build/BUILD/pymol-3.1.0-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 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘have_gamess’: /builddir/build/BUILD/pymol-3.1.0-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]; | ^~~~ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:869:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp:868:9: note: ‘typecheck’ was declared here 868 | int typecheck; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_stats’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_wavefunction’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47: /builddir/build/BUILD/pymol-3.1.0-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) { | ^~~~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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) { | ^~~~~~~~~~~~~~~ /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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70: /builddir/build/BUILD/pymol-3.1.0-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) { | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘read_gamess_rundata’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_coordinates’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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] In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/hash.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_options’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/inthash.c In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_contrl’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_input_structure’: /builddir/build/BUILD/pymol-3.1.0-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)); | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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; | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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)); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_contrl_firefly’: /builddir/build/BUILD/pymol-3.1.0-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)); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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 | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_rundata’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘count_orbitals’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘open_molden_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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)); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~^~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c [ 14%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘read_next_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘open_namdbin_read’: /builddir/build/BUILD/pymol-3.1.0-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 CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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" | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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:970, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: In function ‘*__sprintfieee128’, inlined from ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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_chkieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-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 ‘*__sprintfieee128’, inlined from ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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_chkieee128’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘read_next_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:35: warning: ‘*__sprintf_chkieee128’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 675 | sprintf(answer, "%03x/", d1); | ^ In function ‘*__sprintfieee128’, inlined from ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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_chkieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:779:23: /builddir/build/BUILD/pymol-3.1.0-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 ‘*__sprintfieee128’, inlined from ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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_chkieee128’ 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 ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘read_pdb_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘open_pdb_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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(), | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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 ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘get_atom_radius’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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; | ^~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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; | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:27: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘read_pqr_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘read_pqr_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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; | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function ‘open_rst_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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 -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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; | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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/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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c: In function ‘read_tinker_structure’: /builddir/build/BUILD/pymol-3.1.0-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)); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ~~~~~^~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘open_vasp5xdatcar_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_data’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_metadata’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘open_vaspchgcar_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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) | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘open_vaspoutcar_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_data’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_metadata’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘open_vaspparchg_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘write_vaspposcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘open_vaspposcar_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘open_vaspxdatcar_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘read_vaspxml_structure’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘open_vaspxml_read’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 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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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function ‘vtf_read_bonds’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:72: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include/vmdconio.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void eatline(FILE*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Bezier.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57: /builddir/build/BUILD/pymol-3.1.0-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) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Block.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c: In function ‘read_xyz_structure’: /builddir/build/BUILD/pymol-3.1.0-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)); | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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); | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/CarveHelper.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/ContourSurf.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Crystal.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/CarveHelper.cpp:8: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/Err.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Map.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Map.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Map.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Map.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Field.cpp: In function ‘PyObject* FieldAsNumPyArray(CField*, short int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Field.cpp: In function ‘CField* FieldNewFromPyList(PyMOLGlobals*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/GenericBuffer.cpp: In destructor ‘virtual GenericBuffer::~GenericBuffer()’: /builddir/build/BUILD/pymol-3.1.0-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; 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp: In function ‘void* VLADeleteRaw(void*, int, unsigned int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.cpp: In function ‘void* VLAInsertRaw(void*, int, unsigned int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/MyPNG.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Parse.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp: In function ‘size_t pymol::memory_usage()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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/Pixmap.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/PostProcess.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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++) { | 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-mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderPrg.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.cpp:21: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 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-mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/TTT.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderPrg.cpp:20: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Tracker.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/Triangle.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Texture.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Texture.cpp: In function ‘bool TextureIsCharTextured(PyMOLGlobals*, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-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 -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 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-mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Vector.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Vector.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Vector.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Vector.cpp [ 40%] Building CXX object CMakeFiles/_cmd.dir/layer0/Word.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/Word.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Word.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Word.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Word.cpp [ 40%] Building CXX object CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP 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/builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer0/marching_cubes.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt.h:49, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:39: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt.h:57: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/marching_cubes.cpp: In function ‘void mc::calculateNormals(Mesh&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/CGOGL.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ButMode.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/ButMode.cpp:22: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ButMode.cpp: In function ‘void ButModeFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:40: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/CGORenderer.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘void CheckAttributesForUsage(const CGO*, AttribDataDesc&, AttribDataDesc&, CGO*, bool&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGOGL.cpp:9: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Camera.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/COLLADA.cpp:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘ObjectGadgetRamp* ColorGetRamp(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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()) { | ~~~~~~^~~~~~~~~~~~~~~ [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Font.cpp.o /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorExtFromPyList(PyMOLGlobals*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-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) { | ~~^~~~~~~ /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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Font.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorFromPyList(PyMOLGlobals*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetIndex(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const char* ColorGetName(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetStatus(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘void ColorUpdateFromLut(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const float* ColorGet(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘const float* ColorGetRaw(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp: In function ‘int ColorGetEncoded(PyMOLGlobals*, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-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())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ~~^~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUT.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Control.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:22: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Control.cpp: In function ‘void ControlFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp: In function ‘ExtrudeComputeTangents(CExtrude*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp:742:13: warning: ‘*_62’ may be used uninitialized [-Wmaybe-uninitialized] 742 | *(v1++) = *(v++); /* first segment */ | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp:743:13: warning: ‘MEM[(float *)_62 + 4B]’ may be used uninitialized [-Wmaybe-uninitialized] 743 | *(v1++) = *(v++); | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-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++); | ^~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUT.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUT8x13.cpp [ 47%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUT9x15.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Movie.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontType.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Movie.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/PConv.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp:59: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int WrapperObjectAssignSubScript(PyObject*, PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘void OrthoAddOutput(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘std::unique_ptr makeBgGridImage(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int PAutoBlock(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘int PIsGlutThread()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp: In function ‘void OrthoDoDraw(PyMOLGlobals*, const OrthoDrawInfo&)’: /builddir/build/BUILD/pymol-3.1.0-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); | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PConv.cpp: In function ‘int PConvPyListToBitmask(PyObject*, int*, ov_size)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/PConv.cpp: In function ‘PyObject* PConvLabPosVecToPyList(const std::vector&)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘PLabelAtomAlt(PyMOLGlobals*, AtomInfoType*, char const*, char const*, int)’: /builddir/build/BUILD/pymol-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Pop.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp In file included from /usr/include/string.h:548, from /usr/include/python3.13/Python.h:39, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp:340:13: /usr/include/bits/string_fortified.h:140:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 140 | 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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp:357:13: /usr/include/bits/string_fortified.h:140:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 140 | return __builtin___strcat_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Pop.cpp:22: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Pop.cpp: In function ‘void PopFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Pop.cpp:54:3: note: in expansion of macro ‘DeleteP’ 54 | DeleteP(G->Pop); | ^~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Rep.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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++/15/bits/stl_uninitialized.h:63, from /usr/include/c++/15/memory:71, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:23, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.cpp:17: /usr/include/c++/15/bits/stl_algobase.h:258:5: note: declared here 258 | max(const _Tp& __a, const _Tp& __b) | ^~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:38: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Rep.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘int SceneViewEqual(float*, float*)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/bits/specfun.h:43, from /usr/include/c++/15/cmath:3913, from /usr/include/c++/15/math.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_std.h:24, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:18: /usr/include/c++/15/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:1469:24: required from here 1469 | return std::make_pair(clip.m_front, clip.m_back); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_pair.h:1146:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1146 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp: In function ‘RayTraceThread(_CRayThreadInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:4: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:4: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp: In function ‘void PickColorConverterSetRgbaBitsFromGL(PyMOLGlobals*, PickColorConverter&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.cpp: In function ‘void SceneClickPickBond(PyMOLGlobals*, int, int, int, const NamedPicking&)’: /builddir/build/BUILD/pymol-3.1.0-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) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:323:32: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRay.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRender.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.cpp: In function ‘SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, NamedPicking const&, int, bool)’: /builddir/build/BUILD/pymol-3.1.0-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:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4230, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/pymol/zstring_view.h:12, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.h:4, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:1: In function ‘*__snprintfieee128’, inlined from ‘SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, NamedPicking const&, int, bool)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneMouse.cpp:454:11: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output 21 or more bytes (assuming 276) into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRay.cpp:2: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneView.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRender.cpp:11: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRender.cpp: In function ‘void SceneInitializeViewport(PyMOLGlobals*, bool)’: /builddir/build/BUILD/pymol-3.1.0-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 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 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-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 CMakeFiles/_cmd.dir/layer1/Seq.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp [ 55%] Building CXX object CMakeFiles/_cmd.dir/layer1/Setting.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOp.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOp.cpp: In member function ‘pymol::SymOp::to_string[abi:cxx11]() const’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4230, from /usr/include/c++/15/string:56, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOp.h:9, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOp.cpp:7: In function ‘*__snprintfieee128’, inlined from ‘pymol::SymOp::to_string[abi:cxx11]() const’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOp.cpp:37:16: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 6 and 17 bytes into a destination of size 8 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOpPConv.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/SymOpTools.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: In function ‘int SeqFindRowCol(PyMOLGlobals*, int, int, int*, int*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: In member function ‘virtual void CSeq::reshape(int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: In member function ‘virtual void CSeq::draw(CGO*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.h:21, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp:22: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: In function ‘void SeqFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp:731:3: note: in expansion of macro ‘DeleteP’ 731 | DeleteP(G->Seq); | ^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingUniqueResetAll(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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) | ^~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Text.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Text.cpp.o.d -o 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include 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-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/AssemblyHelpers.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp: In member function ‘virtual void CWizard::draw(CGO*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp:27: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp: In function ‘void WizardFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Wizard.cpp:845:3: note: in expansion of macro ‘DeleteP’ 845 | DeleteP(G->Wizard); | ^~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Text.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.cpp:37: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.cpp: In function ‘bool AtomResiFromResv(char*, size_t, int, char)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:24: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp: In member function ‘void seqvec_t::set(int, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp: In member function ‘const char* seqvec_t::get(int) const’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/DistSet.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/DistSet.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.cpp: In member function ‘int CoordSet::extendIndices(int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/DistSet.cpp: In function ‘int DistSetGetLabelVertex(DistSet*, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/DistSet.cpp: In member function ‘pymol::Result > DistSet::getLabelOffset(int) const’: /builddir/build/BUILD/pymol-3.1.0-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()) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/GadgetSet.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/MmodTyping.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/GadgetSet.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/MmtfMoleculeReader.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/HydrogenAdder.cpp: In function ‘int ObjectMoleculeAddSeleHydrogensRefactored(ObjectMolecule*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/MolV3000.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CifMoleculeReader.cpp:31: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/CifBondDict.h:93:12: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘PyObject* ObjectCGOAllStatesAsPyList(ObjectCGO*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘int ObjectCGOAllStatesFromPyList(ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h: In copy constructor ‘ObjectCGOState::ObjectCGOState(const ObjectCGOState&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromCGO(PyMOLGlobals*, ObjectCGO*, CGO*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGODefine(PyMOLGlobals*, ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromFloatArray(PyMOLGlobals*, ObjectCGO*, float*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCallback.cpp:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp:6: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘void ObjectCurveState::updateRawCGO()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘virtual void ObjectCurve::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In function ‘PyObject* BezierSplineAsPyList(const pymol::BezierSpline&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘PyObject* ObjectCurveState::asPyList() const’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: In member function ‘PyObject* ObjectCurve::statesAsPyList() const’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCurve.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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( | ^~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectGadgetRamp.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘int ObjectDistMoveWithObject(ObjectDist*, ObjectMolecule*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘void ObjectDistUpdateExtents(ObjectDist*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘PyObject* ObjectDistDSetAsPyList(ObjectDist*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘int ObjectDistDSetFromPyList(ObjectDist*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In member function ‘virtual void ObjectDist::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectDist.cpp: In function ‘void ObjectDistInvalidateRep(ObjectDist*, cRep_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectGadget.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectGroup.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectGadgetRamp.cpp:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:36: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:27: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapValidXtal(ObjectMap*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapTrim(ObjectMap*, int, float*, float*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapDouble(ObjectMap*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapHalve(ObjectMap*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘void ObjectMapRegeneratePoints(ObjectMap*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘PyObject* ObjectMapAllStatesAsPyList(ObjectMap*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapAllStatesFromPyList(ObjectMap*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapNewCopy(PyMOLGlobals*, const ObjectMap*, ObjectMap**, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapState* ObjectMapStatePrime(ObjectMap*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘void ObjectMapUpdateExtents(ObjectMap*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapCCP4StrToMap(ObjectMap*, char*, int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapXPLORStrToMap(ObjectMap*, char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapFLDStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapBRIXStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘int ObjectMapACNTStrToMap(ObjectMap*, char*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyBrick(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyMap(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:33: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp: In member function ‘ObjectMesh::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp:28: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 50 and 305 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 27 and 282 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘int ObjectMoleculeFillOpenValences(ObjectMolecule*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:4346:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘intâ€™ [-Wsign-compare] 4346 | if (atm1 >= I->NAtom || atm2 >= I->NAtom) { | ~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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) { | ~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:43: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘std::vector ObjectMoleculeGetMolMappingVec(const ObjectMolecule&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘void ObjectMoleculePBCUnwrap(ObjectMolecule&, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In member function ‘bool ObjectMolecule::atomHasAnyCoordinates(size_t) const’: /builddir/build/BUILD/pymol-3.1.0-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) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMesh.cpp: In function ‘ObjectMeshDump(ObjectMesh*, char const*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output 31 or more bytes (assuming 286) into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:33: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘PyObject* ObjectSliceAllStatesAsPyList(ObjectSlice*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceDrag(ObjectSlice*, int, int, float*, float*, float*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘int ObjectSliceGetVertex(ObjectSlice*, int, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSliceState* ObjectSliceStateGetActive(ObjectSlice*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSlice* ObjectSliceFromMap(PyMOLGlobals*, ObjectSlice*, ObjectMap*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceRecomputeExtent(ObjectSlice*)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:49: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 34 and 289 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp: In function ‘ObjectMapDump(ObjectMap const*, char const*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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:970, from /usr/include/python3.13/Python.h:37, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:21: In function ‘*__snprintfieee128’, inlined from ‘ObjectMapDump(ObjectMap const*, char const*, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:5983:5: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output 30 or more bytes (assuming 285) into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘ObjectSlice::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:44: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 51 and 306 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 28 and 283 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:35: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceInvalidateMapName(ObjectSurface*, const char*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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:970, from /usr/include/python3.13/Python.h:37, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:24: In function ‘*__snprintfieee128’, 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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:334:7: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 26 and 291 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘ObjectMoleculeLoadRSTFile(PyMOLGlobals*, ObjectMolecule*, char const*, int, int, char)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:1304:9: note: ‘buffer’ was declared here 1304 | char *buffer, *p; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘ObjectSurfaceDump(ObjectSurface*, char const*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:45: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output 34 or more bytes (assuming 289) into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepAngle.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4290:3: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 14 and 1037 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int) [clone .isra.0]’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4290:3: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 14 and 1037 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In member function ‘ObjectSurface::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 30 and 285 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In member function ‘ObjectMolecule::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 68 and 333 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:38: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp: In function ‘ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, float const*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10749:14: note: ‘*__sprintfieee128’ 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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘PyObject* ObjectVolumeAllStatesAsPyList(ObjectVolume*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeAllStatesFromPyList(ObjectVolume*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeInvalidateMapName(ObjectVolume*, const char*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::update()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘void ObjectVolumeRecomputeExtent(ObjectVolume*)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 16 and 1039 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepAngle.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 16 and 1039 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 16 and 1039 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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 ‘*__snprintfieee128’, inlined from ‘ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMap.cpp:4836:28: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 16 and 1039 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp: In function ‘ObjectVolumeStateGetMapState(ObjectVolumeState*)’: /builddir/build/BUILD/pymol-3.1.0-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:970, from /usr/include/python3.13/Python.h:37, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:20: In function ‘*__snprintfieee128’, inlined from ‘ObjectVolumeStateGetMapState(ObjectVolumeState*)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectVolume.cpp:79:5: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 46 and 301 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:8569:43: /builddir/build/BUILD/pymol-3.1.0-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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp: In function ‘Rep* RepCartoonNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCylBond.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDihedral.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:338:23: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:25, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.h:25, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:36: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:339:23: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.h:22: In member function ‘pymol::vla::operator+(int)AtomInfoType*’, inlined from ‘GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals*, ObjectMolecule*, CoordSet*, CGO*, CExtrude*, int, int*, float*, float*, float*, CCInOut const*, int*, float*, int, int, float, float) [clone .isra.0]’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1740:34: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:118:60: warning: ‘atom_index2’ may be used uninitialized [-Wmaybe-uninitialized] 118 | template T* operator+(S i) { return m_vla + i; } | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp: In function ‘GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals*, ObjectMolecule*, CoordSet*, CGO*, CExtrude*, int, int*, float*, float*, float*, CCInOut const*, int*, float*, int, int, float, float) [clone .isra.0]’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1594:20: note: ‘atom_index2’ was declared here 1594 | int atom_index1, atom_index2, *s, | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCylBond.cpp:32: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDihedral.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDistDash.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1008:75: 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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:462:11: note: ‘i’ was declared here 462 | int i; | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDistLabel.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDistDash.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepEllipsoid.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDistLabel.cpp:28: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepLabel.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp:32: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.h:22, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.h:21, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp: In function ‘RepDotDoNew(CoordSet*, cRepDot_t, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepLabel.cpp:31: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepMesh.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepNonbonded.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp:30: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphereImmediate.cpp In file included from /usr/include/c++/15/memory:80, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:23, from /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include/pymol/memory.h:47:7, inlined from ‘Isofield::~Isofield()’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Isosurf.h:30:8, inlined from ‘RepMeshNew(CoordSet*, int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepMesh.cpp:1063:5: /usr/include/c++/15/bits/unique_ptr.h:398:19: warning: ‘field’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepMesh.cpp: In function ‘RepMeshNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepMesh.cpp:725:13: note: ‘field’ was declared here 725 | Isofield *field; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp: In function ‘RepRibbonNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:422:15: warning: ‘*_685’ may be used uninitialized [-Wmaybe-uninitialized] 422 | *(v1++) = *(v++); /* first segment */ | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:423:15: warning: ‘MEM[(float *)_685 + 4B]’ may be used uninitialized [-Wmaybe-uninitialized] 423 | *(v1++) = *(v++); | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:424:15: warning: ‘MEM[(float *)_685 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 424 | *(v1++) = *(v++); | ^~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepWireBond.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphere.cpp:34: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphereGenerate.cpp:20: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphereImmediate.cpp:20: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepWireBond.cpp:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:35: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/VFont.cpp.o -MF CMakeFiles/_cmd.dir/layer2/VFont.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/VFont.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/VFont.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/Sculpt.cpp:25: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:25, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:24, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.h:9, from /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:57:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:55:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:49:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp:47:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘SideChainHelperMarkNonCartoonBonded(bool*, ObjectMolecule const*, CoordSet const*, bool, bool)’: /builddir/build/BUILD/pymol-3.1.0-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/layer3/AtomIterators.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 CMakeFiles/_cmd.dir/layer3/AtomIterators.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/AtomIterators.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/AtomIterators.cpp [ 80%] Building CXX object CMakeFiles/_cmd.dir/layer3/CifDataValueFormatter.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT 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-3.1.0-build/pymol-open-source-3.1.0/layer3/CifDataValueFormatter.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/Editor.cpp.o -MF CMakeFiles/_cmd.dir/layer3/Editor.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/Editor.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp [ 80%] Building CXX object CMakeFiles/_cmd.dir/layer3/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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer3/Executive.cpp.o -MF CMakeFiles/_cmd.dir/layer3/Executive.cpp.o.d -o CMakeFiles/_cmd.dir/layer3/Executive.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/AtomIterators.cpp: In member function ‘virtual bool SeleAtomIterator::next()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/AtomIterators.cpp: In member function ‘virtual bool SeleCoordIterator::next()’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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; | ^~~~~~ [ 81%] Building CXX object CMakeFiles/_cmd.dir/layer3/ExecutivePython.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:38: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveRenderSelectionsFromTargets(PyMOLGlobals*, bool, int, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘float ExecutiveRMSPairs(PyMOLGlobals*, const std::vector&, int, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:52: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:27: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) { | ^~ | & [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/Interactions.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:39: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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) | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘EditorPrepareDrag(PyMOLGlobals*, pymol::CObject*, int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:42: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 22 and 277 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.h:27, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Result.h: In constructor ‘pymol::Result::Result(type) [with ResultT = std::pair]’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Result.h:99:3: note: parameter passing for argument of type ‘pymol::Result >::type’ {aka ‘std::pair’} when C++17 is enabled changed to match C++14 in GCC 10.1 99 | Result(type r) : m_result(std::move(r)) {} | ^~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:1: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘EditorDefineExtraPks(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:337:12: note: ‘*__sprintfieee128’ output between 9 and 264 bytes into a destination of size 256 337 | sprintf(buffer, "(byres %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:339:12: note: ‘*__sprintfieee128’ output between 11 and 266 bytes into a destination of size 256 339 | sprintf(buffer, "(bychain %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:341:12: note: ‘*__sprintfieee128’ output between 12 and 267 bytes into a destination of size 256 341 | sprintf(buffer, "(byobject %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Interactions.cpp: In function ‘int pymol::PrepareNeighborTables(PyMOLGlobals*, int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/MoleculeExporter.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/MovieScene.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:17: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Movie.h:24, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/MovieScene.cpp:11: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h:23, from /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:26:26, inlined from ‘MaeExportGetAtomStyle(PyMOLGlobals*, SeleCoordIterator const&)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/MaeExportHelpers.cpp:75:26: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.h: In function ‘MaeExportGetAtomStyle(PyMOLGlobals*, SeleCoordIterator const&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/MoleculeExporter.cpp:24: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/RingFinder.cpp In function ‘ExecutiveGetAdjustedSelectionWidth(PyMOLGlobals*, bool)’, inlined from ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:8414:50: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveRemoveAtoms(PyMOLGlobals*, char const*, int)’: /builddir/build/BUILD/pymol-3.1.0-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", | ^~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:94: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 42 and 307 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-build/pymol-open-source-3.1.0/layer3/RingFinder.cpp: In member function ‘void AbstractRingFinder::recursion(int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ output between 21 and 1298 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:12224:21: note: directive argument in the range [1, 2147483647] /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-build/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp: In function ‘PlugIOManagerLoad’: /builddir/build/BUILD/pymol-3.1.0-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:970, from /usr/include/python3.13/Python.h:37, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_python.h:34, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:21: In function ‘*__snprintfieee128’, inlined from ‘PlugIOManagerLoad’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/PlugIOManager.cpp:940:7: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 58 and 313 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp:29: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerRefresh(PyMOLGlobals*, std::vector&)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.h:21, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp:26: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Seeker.cpp: In function ‘void SeekerFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 84 and 339 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 56 and 311 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 84 and 339 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:41: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In member function ‘virtual bool SelectorAtomIterator::next()’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘bool SelectorIsSelectionDiscrete(PyMOLGlobals*, SelectorID_t, bool)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorClassifyAtoms(PyMOLGlobals*, int, int, ObjectMolecule*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘const char* SelectorGetNameFromIndex(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorColorectionGet(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorColorectionApply(PyMOLGlobals*, PyObject*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorSecretsAsPyList(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘PyObject* SelectorAsPyList(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCountStates(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCheckIntersection(PyMOLGlobals*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorCountAtoms(PyMOLGlobals*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘void SelectorSetDeleteFlagOnSelectionInObject(PyMOLGlobals*, int, ObjectMolecule*, signed char)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int* SelectorGetIndexVLAImpl(PyMOLGlobals*, CSelector*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘void SelectorLogSele(PyMOLGlobals*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetSingleObjectMolecule(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetFirstObjectMolecule(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘ObjectMolecule** SelectorGetObjectMoleculeVLA(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorGetSeleNCSet(PyMOLGlobals*, SelectorID_t)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorGetArrayNCSet(PyMOLGlobals*, const sele_array_t&, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorMapMaskVDW(PyMOLGlobals*, int, ObjectMapState*, float, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorModulate1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorSelect0(PyMOLGlobals*, EvalElem*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘pymol::Result<> SelectorSelect1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorSelect2(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorLogic1(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘int SelectorOperator22(PyMOLGlobals*, EvalElem*, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘pymol::Result > > SelectorEvaluate(PyMOLGlobals*, std::vector >&, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 35 and 300 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 41 and 306 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 49 and 314 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/SelectorTmp.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/SpecRec.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer3/SpecRecSpecial.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:11915:21: note: directive argument in the range [1, 2147483647] /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ output 21 or more bytes (assuming 1044) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ 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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:282:53: note: ‘*__snprintfieee128’ output 32 or more bytes (assuming 287) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer4/Menu.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp:56: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp: In function ‘PyObject* CmdPushUndo(PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp: In function ‘PyObject* CmdGetMinMax(PyObject*, PyObject*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp:65: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp:4017:19: required from here 4017 | return APIResult(G, result); | ~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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) { | ~~^~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer5/PyMOL.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘CExecutive::drag(int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15625:26: note: ‘*__sprintfieee128’ 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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:24, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.h:22, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp:31: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveManageObject(PyMOLGlobals*, pymol::CObject*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 73 and 328 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 61 and 316 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: /builddir/build/BUILD/pymol-3.1.0-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:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4230, from /usr/include/c++/15/string:56, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:20: In function ‘*__snprintfieee128’, inlined from ‘SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:1716:19: /usr/include/bits/stdio2.h:68:35: note: ‘*__snprintf_chkieee128’ output between 59 and 324 bytes into a destination of size 255 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/PyMOL.cpp:35: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layer5/TestPyMOL.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer5/PyMOL.cpp:23: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/PyMOL.cpp: In function ‘void PyMOL_Stop(CPyMOL*)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer5/PyMOL.cpp:2031:3: note: in expansion of macro ‘DeleteP’ 2031 | DeleteP(G->Movie); | ^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 36 and 546 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 67 and 322 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:5727:38: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ output between 56 and 321 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveSetSession(PyMOLGlobals*, _object*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:5727:38: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘*__snprintfieee128’ 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-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/TestPyMOL.cpp:35: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/main.cpp:53: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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 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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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 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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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-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 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Image.cpp [ 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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_List.cpp /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Executive.cpp:3: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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_Picking.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 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CMakeFiles/_cmd.dir/layerCTest/Test_Picking.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Picking.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Picking.cpp [ 92%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Result.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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 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-mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_Result.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Result.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Result.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Result.cpp [ 92%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_ScrollBar.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_ScrollBar.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_ScrollBar.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ScrollBar.cpp [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ShaderPreprocessor.cpp [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.13/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_SymOp.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ShaderPreprocessor.cpp:5: /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-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, | ^~~~~~~~~~ [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_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-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 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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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1497:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1497:24: 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‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1498:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1498:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1499:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1499:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-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-3.1.0-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 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1550:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 4 into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 4 into destination object ‘nx’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1550:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [8, 12] into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 8 into destination object ‘nx’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1551:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 4 into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 4 into destination object ‘ny’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1551:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [8, 12] into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 8 into destination object ‘ny’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1552:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset 4 into destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset 4 into destination object ‘nz’ of size 4 In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, inlined from ‘get_int32’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:606:10, inlined from ‘handle_wrapped_v1’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1552:26, inlined from ‘frame_from_bytes’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1751:29: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:54:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [8, 12] into 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The C compiler identification is GNU 15.0.1 -- The CXX compiler identification is GNU 15.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.7s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ cmake --build . --config Release -j5 /usr/bin/cmake -S/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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/usr/bin/gcc -D_champ_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ -I/usr/include/python3.13 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/vla.c.o -MF CMakeFiles/_champ.dir/contrib/champ/vla.c.o.d -o CMakeFiles/_champ.dir/contrib/champ/vla.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/vla.c [100%] Linking C shared library /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-ppc64le-cpython-313/chempy/champ/_champ.cpython-313-powerpc64le-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/_champ.dir/link.d -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,_champ.cpython-313-powerpc64le-linux-gnu.so -o /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-ppc64le-cpython-313/chempy/champ/_champ.cpython-313-powerpc64le-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-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' [100%] Built target _champ gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ/CMakeFiles 0 running bdist_wheel running build running build_py copying modules/chempy/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/arc.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/bonds.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/brick.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/cc1.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/charge.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/cif.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/cpv.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/dictdb.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/gamess1.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/gms.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/hetatm.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/io.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/lst.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/mae.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/map.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/mass.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/mmd.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/models.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/mol.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/mol2.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/neighbor.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/pdb.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/pkl.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/place.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/protein.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/sdf.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/solvate.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/water_amber.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/water_residues.py -> build/lib.linux-ppc64le-cpython-313/chempy copying modules/chempy/xyz.py -> build/lib.linux-ppc64le-cpython-313/chempy creating build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/scene_bin_gui.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/shortcut_menu_gui.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt creating build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk copying modules/pymol/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/__main__.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/_gui.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/api.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/callback.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/cgo.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/cgobuilder.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/checking.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/cmd.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/colorramping.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/commanding.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/completing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/computing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/constants.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/controlling.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/creating.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/editing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/editor.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/experimenting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/exporting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/externing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/feedingback.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/fitting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/gui.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/headering.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/helping.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/importing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/internal.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/invocation.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/keyboard.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/keywords.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/lazyio.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/locking.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/menu.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/monitoring.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/morphing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/movie.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/moving.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/mpeg_encode.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/parser.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/parsing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/povray.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/preset.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/querying.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/rpc.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/save_shortcut.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/selecting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/selector.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/seqalign.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/setting.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/shortcut.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/shortcut_dict.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/shortcut_manager.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/util.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/vfont.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/viewing.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/wizarding.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/xray.py -> build/lib.linux-ppc64le-cpython-313/pymol copying modules/pymol/xwin.py -> build/lib.linux-ppc64le-cpython-313/pymol creating build/lib.linux-ppc64le-cpython-313/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-ppc64le-cpython-313/pymol2 creating build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-ppc64le-cpython-313/chempy/bmin copying modules/chempy/champ/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-ppc64le-cpython-313/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-ppc64le-cpython-313/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-ppc64le-cpython-313/chempy/champ creating build/lib.linux-ppc64le-cpython-313/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/fast creating build/lib.linux-ppc64le-cpython-313/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/fragments creating build/lib.linux-ppc64le-cpython-313/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-ppc64le-cpython-313/chempy/mmtf creating build/lib.linux-ppc64le-cpython-313/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-ppc64le-cpython-313/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-ppc64le-cpython-313/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-ppc64le-cpython-313/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-ppc64le-cpython-313/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-ppc64le-cpython-313/chempy/tinker creating build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms creating build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax creating build/lib.linux-ppc64le-cpython-313/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/skins creating build/lib.linux-ppc64le-cpython-313/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/startup creating build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/demo creating build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal creating build/lib.linux-ppc64le-cpython-313/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-ppc64le-cpython-313/pymol/Qt creating build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-ppc64le-cpython-313/pymol/plugins creating build/lib.linux-ppc64le-cpython-313/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol/stereochemistry creating build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-ppc64le-cpython-313/pymol/wizard creating build/lib.linux-ppc64le-cpython-313/web creating build/lib.linux-ppc64le-cpython-313/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-ppc64le-cpython-313/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-ppc64le-cpython-313/web/examples creating build/lib.linux-ppc64le-cpython-313/pymol_web creating build/lib.linux-ppc64le-cpython-313/pymol_web/examples copying modules/pymol_web/examples/__init__.py -> build/lib.linux-ppc64le-cpython-313/pymol_web/examples copying modules/pymol_web/examples/justhttpd.py -> build/lib.linux-ppc64le-cpython-313/pymol_web/examples running egg_info creating modules/pymol.egg-info writing modules/pymol.egg-info/PKG-INFO /usr/lib/python3.13/site-packages/setuptools/_core_metadata.py:161: 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/askpartial.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/change_confirm.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/create_shortcut.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/help_shortcut.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/shortcut_menu.ui -> build/lib.linux-ppc64le-cpython-313/pmg_qt/forms running build_ext cmake /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -DTARGET_NAME=_cmd -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-ppc64le-cpython-313/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/python3.13/site-packages/numpy/_core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.13;/usr/include/python3.13; -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-313-powerpc64le-linux-gnu.so -- Configuring done (0.0s) -- Generating done (0.1s) -- Build files have been written to: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd cmake --build . --config Release -j5 /usr/bin/cmake -S/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd/CMakeFiles/_cmd.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' gmake[2]: Nothing to be done for 'CMakeFiles/_cmd.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' [100%] Built target _cmd gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_cmd/CMakeFiles 0 cmake /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -DTARGET_NAME=_champ -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-ppc64le-cpython-313/chempy/champ -DCMAKE_BUILD_TYPE=Release -DALL_INC_DIR=contrib/champ;/usr/include/python3.13;/usr/include/python3.13; -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-313-powerpc64le-linux-gnu.so -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ cmake --build . --config Release -j5 /usr/bin/cmake -S/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 -B/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' /usr/bin/gmake -f CMakeFiles/_champ.dir/build.make CMakeFiles/_champ.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ/CMakeFiles/_champ.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' /usr/bin/gmake -f CMakeFiles/_champ.dir/build.make CMakeFiles/_champ.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' gmake[2]: Nothing to be done for 'CMakeFiles/_champ.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' [100%] Built target _champ gmake[1]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-ppc64le-cpython-313/_champ/CMakeFiles 0 installing to build/bdist.linux-ppc64le/wheel running install running install_lib creating build/bdist.linux-ppc64le creating build/bdist.linux-ppc64le/wheel creating build/bdist.linux-ppc64le/wheel/pymol copying build/lib.linux-ppc64le-cpython-313/pymol/_cmd.cpython-313-powerpc64le-linux-gnu.so -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/__main__.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/_gui.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/api.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/callback.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/cgo.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/cgobuilder.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/checking.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/cmd.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/colorprinting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/colorramping.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/commanding.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/completing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/computing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/constants.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/constants_palette.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/controlling.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/creating.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/diagnosing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/editing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/editor.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/experimenting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/exporting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/externing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/feedingback.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/fitting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/gui.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/headering.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/helping.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/importing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/internal.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/invocation.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/keyboard.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/keywords.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/lazyio.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/locking.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/menu.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/monitoring.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/morphing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/movie.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/moving.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/mpeg_encode.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/parser.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/parsing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/povray.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/preset.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/pymolhttpd.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/querying.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/rpc.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/save_shortcut.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/selecting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/selector.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/seqalign.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/setting.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/shortcut.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/shortcut_dict.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/shortcut_manager.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/util.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/vfont.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/viewing.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/wizarding.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/xray.py -> build/bdist.linux-ppc64le/wheel/./pymol copying build/lib.linux-ppc64le-cpython-313/pymol/xwin.py -> build/bdist.linux-ppc64le/wheel/./pymol creating build/bdist.linux-ppc64le/wheel/pymol/Qt copying build/lib.linux-ppc64le-cpython-313/pymol/Qt/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol/Qt copying build/lib.linux-ppc64le-cpython-313/pymol/Qt/utils.py -> build/bdist.linux-ppc64le/wheel/./pymol/Qt creating build/bdist.linux-ppc64le/wheel/pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/installation.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/legacysupport.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/managergui.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/managergui_qt.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins copying build/lib.linux-ppc64le-cpython-313/pymol/plugins/repository.py -> build/bdist.linux-ppc64le/wheel/./pymol/plugins creating build/bdist.linux-ppc64le/wheel/pymol/stereochemistry copying build/lib.linux-ppc64le-cpython-313/pymol/stereochemistry/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol/stereochemistry creating build/bdist.linux-ppc64le/wheel/pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/annotation.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/appearance.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/benchmark.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/box.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/charge.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/cleanup.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/command.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/demo.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/density.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/distance.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/dragging.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/filter.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/label.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/measurement.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/message.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/mutagenesis.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/nucmutagenesis.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/openvr.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/pair_fit.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/pseudoatom.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/renaming.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/sculpting.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/security.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/stereodemo.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard copying build/lib.linux-ppc64le-cpython-313/pymol/wizard/toggle.py -> build/bdist.linux-ppc64le/wheel/./pymol/wizard creating build/bdist.linux-ppc64le/wheel/chempy creating build/bdist.linux-ppc64le/wheel/chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/champ/_champ.cpython-313-powerpc64le-linux-gnu.so -> build/bdist.linux-ppc64le/wheel/./chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/champ/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/champ/amber99.py -> build/bdist.linux-ppc64le/wheel/./chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/champ/assign.py -> build/bdist.linux-ppc64le/wheel/./chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/champ/formal_charges.py -> build/bdist.linux-ppc64le/wheel/./chempy/champ copying build/lib.linux-ppc64le-cpython-313/chempy/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/arc.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/bond_amber.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/bond_mmff.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/bonds.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/brick.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/cc1.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/charge.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/cif.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/cpv.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/dictdb.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/gamess1.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/gms.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/hetatm.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/io.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/lst.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/mae.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/map.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/mass.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/mmd.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/models.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/mol.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/mol2.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/neighbor.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/pdb.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/pkl.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/place.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/protein.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/protein_amber.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/protein_amber99.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/protein_mmff.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/protein_residues.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/sdf.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/solvate.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/water_amber.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/water_residues.py -> build/bdist.linux-ppc64le/wheel/./chempy copying build/lib.linux-ppc64le-cpython-313/chempy/xyz.py -> build/bdist.linux-ppc64le/wheel/./chempy creating build/bdist.linux-ppc64le/wheel/chempy/bmin copying build/lib.linux-ppc64le-cpython-313/chempy/bmin/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/bmin copying build/lib.linux-ppc64le-cpython-313/chempy/bmin/commands.py -> build/bdist.linux-ppc64le/wheel/./chempy/bmin copying build/lib.linux-ppc64le-cpython-313/chempy/bmin/realtime.py -> build/bdist.linux-ppc64le/wheel/./chempy/bmin copying build/lib.linux-ppc64le-cpython-313/chempy/bmin/state.py -> build/bdist.linux-ppc64le/wheel/./chempy/bmin copying build/lib.linux-ppc64le-cpython-313/chempy/bmin/util.py -> build/bdist.linux-ppc64le/wheel/./chempy/bmin creating build/bdist.linux-ppc64le/wheel/chempy/fast copying build/lib.linux-ppc64le-cpython-313/chempy/fast/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/fast creating build/bdist.linux-ppc64le/wheel/chempy/fragments copying build/lib.linux-ppc64le-cpython-313/chempy/fragments/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/fragments creating build/bdist.linux-ppc64le/wheel/chempy/mmtf copying build/lib.linux-ppc64le-cpython-313/chempy/mmtf/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/mmtf copying build/lib.linux-ppc64le-cpython-313/chempy/mmtf/io.py -> build/bdist.linux-ppc64le/wheel/./chempy/mmtf creating build/bdist.linux-ppc64le/wheel/chempy/tinker copying build/lib.linux-ppc64le-cpython-313/chempy/tinker/__init__.py -> build/bdist.linux-ppc64le/wheel/./chempy/tinker copying build/lib.linux-ppc64le-cpython-313/chempy/tinker/amber.py -> build/bdist.linux-ppc64le/wheel/./chempy/tinker copying build/lib.linux-ppc64le-cpython-313/chempy/tinker/keyword.py -> build/bdist.linux-ppc64le/wheel/./chempy/tinker copying build/lib.linux-ppc64le-cpython-313/chempy/tinker/realtime.py -> build/bdist.linux-ppc64le/wheel/./chempy/tinker copying build/lib.linux-ppc64le-cpython-313/chempy/tinker/state.py -> build/bdist.linux-ppc64le/wheel/./chempy/tinker creating build/bdist.linux-ppc64le/wheel/pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/TextEditor.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/advanced_settings_gui.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/builder.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/file_dialogs.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/keymapping.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/mimic_pmg_tk.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/mimic_tk.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/properties_dialog.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/pymol_gl_widget.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/pymol_qt_gui.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/scene_bin_gui.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/shortcut_menu_gui.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt copying build/lib.linux-ppc64le-cpython-313/pmg_qt/volume.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt creating build/bdist.linux-ppc64le/wheel/pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/askpartial.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/change_confirm.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/colors.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/create_shortcut.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/fetch.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/help_shortcut.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/load_aln.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/load_mae.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/load_map.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/load_mtz.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/load_traj.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/movieexport.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/pluginitem.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/pluginmanager.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/png.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/props.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/render.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/save_molecule.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/save_object.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms copying build/lib.linux-ppc64le-cpython-313/pmg_qt/forms/shortcut_menu.ui -> build/bdist.linux-ppc64le/wheel/./pmg_qt/forms creating build/bdist.linux-ppc64le/wheel/pmg_qt/syntax copying build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt/syntax copying build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax/pml.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt/syntax copying build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax/pmlparser.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt/syntax copying build/lib.linux-ppc64le-cpython-313/pmg_qt/syntax/python.py -> build/bdist.linux-ppc64le/wheel/./pmg_qt/syntax creating build/bdist.linux-ppc64le/wheel/pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/ColorEditor.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/Demo.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/PMGApp.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/PyMOLMapLoad.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/SetEditor.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/Setting.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/TextEditor.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk copying build/lib.linux-ppc64le-cpython-313/pmg_tk/volume.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk creating build/bdist.linux-ppc64le/wheel/pmg_tk/skins copying build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/skins creating build/bdist.linux-ppc64le/wheel/pmg_tk/skins/demo copying build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/demo/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/skins/demo creating build/bdist.linux-ppc64le/wheel/pmg_tk/skins/normal copying build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal/ModalWindow.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/skins/normal copying build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/skins/normal copying build/lib.linux-ppc64le-cpython-313/pmg_tk/skins/normal/builder.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/skins/normal creating build/bdist.linux-ppc64le/wheel/pmg_tk/startup copying build/lib.linux-ppc64le-cpython-313/pmg_tk/startup/__init__.py -> build/bdist.linux-ppc64le/wheel/./pmg_tk/startup creating build/bdist.linux-ppc64le/wheel/pymol2 copying build/lib.linux-ppc64le-cpython-313/pymol2/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol2 copying build/lib.linux-ppc64le-cpython-313/pymol2/cmd2.py -> build/bdist.linux-ppc64le/wheel/./pymol2 creating build/bdist.linux-ppc64le/wheel/web creating build/bdist.linux-ppc64le/wheel/web/examples copying build/lib.linux-ppc64le-cpython-313/web/examples/__init__.py -> build/bdist.linux-ppc64le/wheel/./web/examples copying build/lib.linux-ppc64le-cpython-313/web/examples/justhttpd.py -> build/bdist.linux-ppc64le/wheel/./web/examples creating build/bdist.linux-ppc64le/wheel/pymol_web creating build/bdist.linux-ppc64le/wheel/pymol_web/examples copying build/lib.linux-ppc64le-cpython-313/pymol_web/examples/__init__.py -> build/bdist.linux-ppc64le/wheel/./pymol_web/examples copying build/lib.linux-ppc64le-cpython-313/pymol_web/examples/justhttpd.py -> build/bdist.linux-ppc64le/wheel/./pymol_web/examples running install_egg_info Copying modules/pymol.egg-info to build/bdist.linux-ppc64le/wheel/./pymol-3.1.0-py3.13.egg-info running install_scripts creating build/bdist.linux-ppc64le/wheel/pymol/pymol_path copying LICENSE -> build/bdist.linux-ppc64le/wheel/./pymol/pymol_path copying data -> build/bdist.linux-ppc64le/wheel/./pymol/pymol_path/data copying test -> build/bdist.linux-ppc64le/wheel/./pymol/pymol_path/test copying examples -> build/bdist.linux-ppc64le/wheel/./pymol/pymol_path/examples creating build/bdist.linux-ppc64le/wheel/pymol-3.1.0.data creating build/bdist.linux-ppc64le/wheel/pymol-3.1.0.data/scripts creating build/bdist.linux-ppc64le/wheel/pymol-3.1.0.dist-info/WHEEL creating '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir/pip-modern-metadata-xbkwd_xj/.tmp-5bgvfly2/pymol-3.1.0-cp313-cp313-linux_ppc64le.whl' and adding 'build/bdist.linux-ppc64le/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-313-powerpc64le-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-313-powerpc64le-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-ppc64le/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-cp313-cp313-linux_ppc64le.whl size=44838343 sha256=2278dfe3e94149e08c170cb62c3ac665a74b14aba4f811b89bf330a53d2059dc Stored in directory: /builddir/.cache/pip/wheels/76/31/1e/6f5cd56105c073bb26575f1dca286d4ddf8f22443b89981604 Successfully built pymol + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MbiPfl + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-build + '[' /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/pymol-3.1.0-build + mkdir /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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-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-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir/pymol-3.1.0-cp313-cp313-linux_ppc64le.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-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT --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-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir pymol==3.1.0 Using pip 24.3.1 from /usr/lib/python3.13/site-packages/pip (python 3.13) Looking in links: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir Processing ./pyproject-wheeldir/pymol-3.1.0-cp313-cp313-linux_ppc64le.whl Installing collected packages: pymol Creating /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin changing mode of /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin/pymol to 755 Successfully installed pymol-3.1.0 + '[' -d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin ']' + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin/pymol /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin/pymol: updating + rm -rfv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin/__pycache__ + rm -f /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages '!=' /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' -d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages ']' + site_dirs+=("/usr/lib64/python3.13/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/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/BUILD/pymol-3.1.0-build/BUILDROOT --record /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info/RECORD --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-record + rm -fv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info/RECORD removed '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info/RECORD' + rm -fv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info/REQUESTED removed '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol-3.1.0.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-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-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-files --output-modules /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-modules --buildroot /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT --sitelib /usr/lib/python3.13/site-packages --sitearch /usr/lib64/python3.13/site-packages --python-version 3.13 --pyproject-record /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-3.fc42.ppc64le-pyproject-record --prefix /usr pymol chempy web pymol2 pymol_web pmg_tk pmg_qt + cp -a testing /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/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/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py: updating + echo '#!/bin/sh' + echo 'export PYMOL_PATH=/usr/lib64/python3.13/site-packages/pymol' + echo 'exec /usr/bin/python3 /usr/lib64/python3.13/site-packages/pymol/__init__.py "$@"' + mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/data/pymol/icons + touch /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/data/pymol/icons/icon2.svg + ln -sfr /usr/lib64/python3.13/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/data/pymol/icons/icon2.svg + mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin + install -p -m 755 pymol /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin/ + desktop-file-install --vendor= --dir=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/applications /builddir/build/SOURCES/pymol.desktop + mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/pixmaps + install -p -m 644 /builddir/build/SOURCES/pymol.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/pixmaps/ + mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/metainfo + install -p -m 644 /builddir/build/SOURCES/pymol.appdata.xml /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/metainfo/ + appstream-util validate-relax --nonet /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT//usr/share/metainfo/pymol.appdata.xml /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT//usr/share/metainfo/pymol.appdata.xml: OK + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 3.1.0-3.fc42 --unique-debug-suffix -3.1.0-3.fc42.ppc64le --unique-debug-src-base pymol-3.1.0-3.fc42.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/pymol-3.1.0-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-3.1.0-3.fc42.ppc64le 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 mangling shebang in /usr/bin/pymol from /bin/sh to #!/usr/bin/sh *** WARNING: ./usr/src/debug/pymol-3.1.0-3.fc42.ppc64le/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-3.fc42.ppc64le/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-3.fc42.ppc64le/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-3.fc42.ppc64le/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j5 Bytecompiling .py files below /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13 using python3.13 /usr/lib64/python3.13/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.13/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.13/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.13/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: invalid escape sequence '\*' /usr/lib64/python3.13/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: invalid escape sequence '\=' /usr/lib64/python3.13/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: invalid escape sequence '\=' Bytecompiling .py files below /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j5 /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/bmin/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/bmin/__pycache__/commands.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/bmin/__pycache__/util.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/bmin/__pycache__/state.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/bmin/__pycache__/realtime.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/champ/__pycache__/formal_charges.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/champ/__pycache__/assign.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/fragments/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/fast/__pycache__/__init__.cpython-313.pyc: 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/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/web/examples/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol_web/examples/__pycache__/justhttpd.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol2/__pycache__/cmd2.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/testing/tests/undo/api/__pycache__/test_undo_editing.cpython-313.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/web/examples/__pycache__/justhttpd.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/testing/__pycache__/testing.cpython-313.pyc: rewriting with normalized contents Scanned 193 directories and 2222 files, processed 443 inodes, 443 modified (54 replaced + 389 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/pymol-3.1.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.COxQXS + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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-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/BUILD/pymol-3.1.0-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.13/site-packages + _PYTHONSITE=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.13/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-3.1.0-3.fc42.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.sX5Uyl + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-build + cd pymol-open-source-3.1.0 + DOCDIR=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/AUTHORS /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/DEVELOPERS /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/README.md /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + cp -pr /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ChangeLog /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/share/doc/pymol + RPM_EC=0 ++ jobs -p + exit 0 Provides: PyMOL = 3.1.0-3.fc42 application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 3.1.0-3.fc42 pymol(ppc-64) = 3.1.0-3.fc42 python-pymol = 3.1.0-3.fc42 python3-pymol = 3.1.0-3.fc42 python3.13-pymol = 3.1.0-3.fc42 python3.13dist(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: (python3.13dist(numpy) < 3~~ with python3.13dist(numpy) >= 1.26.4) /usr/bin/sh ld64.so.2()(64bit) ld64.so.2(GLIBC_2.23)(64bit) libGL.so.1()(64bit) libGLEW.so.2.2()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_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_2.17)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.32)(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) = 3.13 rtld(GNU_HASH) Processing files: pymol+tests-3.1.0-3.fc42.ppc64le Provides: pymol+tests = 3.1.0-3.fc42 pymol+tests(ppc-64) = 3.1.0-3.fc42 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) = 3.13 Processing files: pymol-debugsource-3.1.0-3.fc42.ppc64le Provides: pymol-debugsource = 3.1.0-3.fc42 pymol-debugsource(ppc-64) = 3.1.0-3.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-3.1.0-3.fc42.ppc64le Provides: debuginfo(build-id) = 40fef0859bea7b51e2b4808e49d7273da1d6c2a8 debuginfo(build-id) = d5b670f3fe22200db1dcfa2a1a74da06a44e40f5 pymol-debuginfo = 3.1.0-3.fc42 pymol-debuginfo(ppc-64) = 3.1.0-3.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(ppc-64) = 3.1.0-3.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT Wrote: /builddir/build/SRPMS/pymol-3.1.0-3.fc42.src.rpm Wrote: /builddir/build/RPMS/pymol-3.1.0-3.fc42.ppc64le.rpm Wrote: /builddir/build/RPMS/pymol+tests-3.1.0-3.fc42.ppc64le.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-3.1.0-3.fc42.ppc64le.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-3.1.0-3.fc42.ppc64le.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Vmerl1 + umask 022 + cd /builddir/build/BUILD/pymol-3.1.0-build + test -d /builddir/build/BUILD/pymol-3.1.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/pymol-3.1.0-build + rm -rf /builddir/build/BUILD/pymol-3.1.0-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild pymol-3.1.0-3.fc42.src.rpm Finish: build phase for pymol-3.1.0-3.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-ppc64le-1738674685.498307/root/var/log/dnf5.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-3.1.0-3.fc42.src.rpm) Config(child) 5 minutes 39 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-debugsource", "epoch": null, "version": "3.1.0", "release": "3.fc42", "arch": "ppc64le" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "3.fc42", "arch": "ppc64le" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "3.fc42", "arch": "src" }, { "name": "pymol+tests", "epoch": null, "version": "3.1.0", "release": "3.fc42", "arch": "ppc64le" }, { "name": "pymol-debuginfo", "epoch": null, "version": "3.1.0", "release": "3.fc42", "arch": "ppc64le" } ] } RPMResults finished