Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c10f' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-vwtu97eg/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-vwtu97eg/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1748989340.287934 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.2 starting (python version = 3.13.0, NVR = mock-6.2-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-vwtu97eg/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-vwtu97eg/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1748989340.287934 -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-vwtu97eg/pymol/pymol.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.2 INFO: Mock Version: 6.2 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1748989340.287934/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:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-5a12c36d-3b2c-47dd-8adf-16f19d4fd0d1 INFO: Checking that a0a6c271b15cccce9f614e595b19f3aa040b118c6c5a7ea25ac8526cbc89023c image matches host's architecture INFO: Copy content of container a0a6c271b15cccce9f614e595b19f3aa040b118c6c5a7ea25ac8526cbc89023c to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1748989340.287934/root INFO: mounting a0a6c271b15cccce9f614e595b19f3aa040b118c6c5a7ea25ac8526cbc89023c with podman image mount INFO: image a0a6c271b15cccce9f614e595b19f3aa040b118c6c5a7ea25ac8526cbc89023c as /var/lib/containers/storage/overlay/924ef891ec91ee0771a2b9d0657c1a1c351e60cb77aadd56573546c5375767d7/merged INFO: umounting image a0a6c271b15cccce9f614e595b19f3aa040b118c6c5a7ea25ac8526cbc89023c (/var/lib/containers/storage/overlay/924ef891ec91ee0771a2b9d0657c1a1c351e60cb77aadd56573546c5375767d7/merged) with podman image umount INFO: Removing image mock-bootstrap-5a12c36d-3b2c-47dd-8adf-16f19d4fd0d1 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-rawhide-x86_64-1748989340.287934/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-5.99.90-5.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 dnf5-5.2.13.1-2.fc43.x86_64 dnf5-plugins-5.2.13.1-2.fc43.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 18.0 MiB/s | 21.7 MiB | 00m01s Copr repository 100% | 29.4 MiB/s | 5.9 MiB | 00m00s Coprdir repository 100% | 12.1 KiB/s | 1.6 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-3.fc43 fedora 8.2 MiB bzip2 x86_64 1.0.8-20.fc42 fedora 99.3 KiB coreutils x86_64 9.7-3.fc43 fedora 5.4 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.12-2.fc43 fedora 1.6 MiB fedora-release-common noarch 43-0.16 fedora 20.4 KiB findutils x86_64 1:4.10.0-5.fc42 fedora 1.9 MiB gawk x86_64 5.3.2-1.fc43 fedora 1.8 MiB glibc-minimal-langpack x86_64 2.41.9000-15.fc43 fedora 0.0 B grep x86_64 3.12-1.fc43 fedora 1.0 MiB gzip x86_64 1.13-3.fc42 fedora 392.9 KiB info x86_64 7.2-3.fc42 fedora 357.9 KiB patch x86_64 2.8-1.fc43 fedora 226.8 KiB redhat-rpm-config noarch 343-6.fc43 fedora 181.4 KiB rpm-build x86_64 5.99.90-5.fc43 fedora 281.7 KiB sed x86_64 4.9-4.fc42 fedora 857.3 KiB shadow-utils x86_64 2:4.17.4-1.fc43 fedora 4.0 MiB tar x86_64 2:1.35-5.fc42 fedora 3.0 MiB unzip x86_64 6.0-66.fc42 fedora 390.3 KiB util-linux x86_64 2.40.4-7.fc43 fedora 3.4 MiB which x86_64 2.23-1.fc42 fedora 83.4 KiB xz x86_64 1:5.8.1-1.fc43 fedora 1.3 MiB Installing dependencies: add-determinism x86_64 0.6.0-1.fc43 fedora 2.5 MiB alternatives x86_64 1.33-1.fc43 fedora 62.2 KiB ansible-srpm-macros noarch 1-17.1.fc42 fedora 35.7 KiB audit-libs x86_64 4.0.4-2.fc43 fedora 351.2 KiB binutils x86_64 2.44-3.fc43 fedora 25.9 MiB build-reproducibility-srpm-macros noarch 0.6.0-1.fc43 fedora 735.0 B bzip2-libs x86_64 1.0.8-20.fc42 fedora 84.6 KiB ca-certificates noarch 2024.2.69_v8.0.401-5.fc42 fedora 2.6 MiB coreutils-common x86_64 9.7-3.fc43 fedora 11.3 MiB crypto-policies noarch 20250602-1.git9a48d06.fc43 fedora 142.6 KiB curl x86_64 8.14.0-1.fc43 fedora 469.9 KiB cyrus-sasl-lib x86_64 2.1.28-30.fc42 fedora 2.3 MiB debugedit x86_64 5.1-6.fc43 fedora 192.7 KiB dwz x86_64 0.15-9.fc42 fedora 291.0 KiB ed x86_64 1.21-2.fc42 fedora 146.5 KiB efi-srpm-macros noarch 6-3.fc43 fedora 40.1 KiB elfutils x86_64 0.193-2.fc43 fedora 2.9 MiB elfutils-debuginfod-client x86_64 0.193-2.fc43 fedora 83.9 KiB elfutils-default-yama-scope noarch 0.193-2.fc43 fedora 1.8 KiB elfutils-libelf x86_64 0.193-2.fc43 fedora 1.2 MiB elfutils-libs x86_64 0.193-2.fc43 fedora 683.4 KiB fedora-gpg-keys noarch 43-0.2 fedora 129.0 KiB fedora-release noarch 43-0.16 fedora 0.0 B fedora-release-identity-basic noarch 43-0.16 fedora 664.0 B fedora-repos noarch 43-0.2 fedora 4.9 KiB fedora-repos-rawhide noarch 43-0.2 fedora 2.2 KiB file x86_64 5.46-4.fc43 copr_base 100.2 KiB file-libs x86_64 5.46-4.fc43 copr_base 11.9 MiB filesystem x86_64 3.18-44.fc43 fedora 112.0 B filesystem-srpm-macros noarch 3.18-44.fc43 fedora 38.2 KiB fonts-srpm-macros noarch 1:2.0.5-22.fc43 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-2.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-14.fc42 fedora 144.0 B gdb-minimal x86_64 16.3-1.fc43 fedora 13.2 MiB gdbm-libs x86_64 1:1.23-9.fc42 fedora 129.9 KiB ghc-srpm-macros noarch 1.9.2-2.fc42 fedora 779.0 B glibc x86_64 2.41.9000-15.fc43 fedora 6.7 MiB glibc-common x86_64 2.41.9000-15.fc43 fedora 1.0 MiB glibc-gconv-extra x86_64 2.41.9000-15.fc43 fedora 7.2 MiB gmp x86_64 1:6.3.0-3.fc43 fedora 819.2 KiB gnat-srpm-macros noarch 6-7.fc42 fedora 1.0 KiB gnupg2 x86_64 2.4.8-2.fc43 fedora 6.5 MiB gnupg2-dirmngr x86_64 2.4.8-2.fc43 fedora 618.4 KiB gnupg2-gpg-agent x86_64 2.4.8-2.fc43 fedora 671.4 KiB gnupg2-gpgconf x86_64 2.4.8-2.fc43 fedora 250.0 KiB gnupg2-keyboxd x86_64 2.4.8-2.fc43 fedora 201.4 KiB gnupg2-verify x86_64 2.4.8-2.fc43 fedora 348.5 KiB gnutls x86_64 3.8.9-5.fc43 fedora 3.6 MiB go-srpm-macros noarch 3.6.0-7.fc43 fedora 60.8 KiB gpgverify noarch 2.1-3.fc43 fedora 8.7 KiB ima-evm-utils-libs x86_64 1.6.2-5.fc43 fedora 60.7 KiB jansson x86_64 2.14-2.fc42 fedora 93.1 KiB java-srpm-macros noarch 1-3.fc43 fedora 102.0 B json-c x86_64 0.18-2.fc42 fedora 86.7 KiB kernel-srpm-macros noarch 1.0-25.fc42 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-5.fc42 fedora 58.3 KiB krb5-libs x86_64 1.21.3-5.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-3.fc42 fedora 38.3 KiB libarchive x86_64 3.8.1-1.fc43 fedora 951.1 KiB libassuan x86_64 2.5.7-3.fc42 fedora 167.8 KiB libattr x86_64 2.5.2-5.fc42 fedora 27.1 KiB libblkid x86_64 2.40.4-7.fc43 fedora 262.4 KiB libbrotli x86_64 1.1.0-7.fc43 copr_base 833.3 KiB libcap x86_64 2.76-1.fc43 fedora 209.2 KiB libcap-ng x86_64 0.8.5-4.fc42 fedora 72.9 KiB libcom_err x86_64 1.47.2-3.fc42 fedora 67.1 KiB libcurl x86_64 8.14.0-1.fc43 fedora 895.2 KiB libeconf x86_64 0.7.6-1.fc43 fedora 64.6 KiB libevent x86_64 2.1.12-15.fc42 fedora 903.1 KiB libfdisk x86_64 2.40.4-7.fc43 fedora 372.3 KiB libffi x86_64 3.4.8-1.fc43 fedora 83.0 KiB libfsverity x86_64 1.6-2.fc42 fedora 32.5 KiB libgcc x86_64 15.1.1-2.fc43 fedora 266.6 KiB libgcrypt x86_64 1.11.1-1.fc43 fedora 1.6 MiB libgomp x86_64 15.1.1-2.fc43 fedora 539.1 KiB libgpg-error x86_64 1.55-1.fc43 fedora 915.3 KiB libidn2 x86_64 2.3.8-1.fc43 fedora 552.5 KiB libksba x86_64 1.6.7-3.fc42 fedora 402.5 KiB libmount x86_64 2.40.4-7.fc43 fedora 356.2 KiB libnghttp2 x86_64 1.65.0-1.fc43 fedora 162.2 KiB libpkgconf x86_64 2.3.0-2.fc42 fedora 78.1 KiB libpsl x86_64 0.21.5-5.fc42 fedora 76.4 KiB libselinux x86_64 3.8-3.fc43 copr_base 193.1 KiB libsemanage x86_64 3.8.1-3.fc43 copr_base 304.4 KiB libsepol x86_64 3.8-1.fc42 fedora 826.0 KiB libsmartcols x86_64 2.40.4-7.fc43 fedora 180.4 KiB libssh x86_64 0.11.1-4.fc42 fedora 565.5 KiB libssh-config noarch 0.11.1-4.fc42 fedora 277.0 B libstdc++ x86_64 15.1.1-2.fc43 fedora 2.8 MiB libtasn1 x86_64 4.20.0-1.fc43 fedora 176.3 KiB libtool-ltdl x86_64 2.5.4-4.fc42 fedora 70.1 KiB libunistring x86_64 1.1-9.fc42 fedora 1.7 MiB libusb1 x86_64 1.0.28-2.fc43 fedora 171.0 KiB libuuid x86_64 2.40.4-7.fc43 fedora 37.3 KiB libverto x86_64 0.3.2-10.fc42 fedora 25.4 KiB libxcrypt x86_64 4.4.38-7.fc43 fedora 284.5 KiB libxml2 x86_64 2.12.10-1.fc43 fedora 1.7 MiB libzstd x86_64 1.5.7-1.fc43 fedora 807.8 KiB lua-libs x86_64 5.4.7-3.fc43 fedora 276.9 KiB lua-srpm-macros noarch 1-15.fc42 fedora 1.3 KiB lz4-libs x86_64 1.10.0-2.fc42 fedora 157.4 KiB mpfr x86_64 4.2.2-1.fc43 fedora 828.8 KiB ncurses-base noarch 6.5-5.20250125.fc42 fedora 326.8 KiB ncurses-libs x86_64 6.5-5.20250125.fc42 fedora 946.3 KiB nettle x86_64 3.10.1-1.fc43 fedora 790.5 KiB npth x86_64 1.8-2.fc42 fedora 49.6 KiB ocaml-srpm-macros noarch 10-4.fc42 fedora 1.9 KiB openblas-srpm-macros noarch 2-19.fc42 fedora 112.0 B openldap x86_64 2.6.9-5.fc43 fedora 655.1 KiB openssl-libs x86_64 1:3.5.0-3.fc43 fedora 8.9 MiB p11-kit x86_64 0.25.5-8.fc43 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-8.fc43 fedora 395.5 KiB package-notes-srpm-macros noarch 0.5-13.fc42 fedora 1.6 KiB pam-libs x86_64 1.7.0-4.fc42 fedora 126.7 KiB pcre2 x86_64 10.45-1.fc43 fedora 697.7 KiB pcre2-syntax noarch 10.45-1.fc43 fedora 273.9 KiB perl-srpm-macros noarch 1-57.fc42 fedora 861.0 B pkgconf x86_64 2.3.0-2.fc42 fedora 88.5 KiB pkgconf-m4 noarch 2.3.0-2.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-2.fc42 fedora 989.0 B popt x86_64 1.19-8.fc42 fedora 132.8 KiB publicsuffix-list-dafsa noarch 20250116-1.fc42 fedora 68.5 KiB pyproject-srpm-macros noarch 1.18.1-1.fc43 copr_base 1.9 KiB python-srpm-macros noarch 3.13-5.fc43 fedora 51.7 KiB qt5-srpm-macros noarch 5.15.17-1.fc43 fedora 500.0 B qt6-srpm-macros noarch 6.9.0-2.fc43 fedora 464.0 B readline x86_64 8.2-13.fc43 fedora 485.0 KiB rpm x86_64 5.99.90-5.fc43 fedora 3.1 MiB rpm-build-libs x86_64 5.99.90-5.fc43 fedora 264.4 KiB rpm-libs x86_64 5.99.90-5.fc43 fedora 929.8 KiB rpm-sequoia x86_64 1.8.0-1.fc43 fedora 2.5 MiB rpm-sign-libs x86_64 5.99.90-5.fc43 fedora 39.7 KiB rust-srpm-macros noarch 26.3-4.fc42 fedora 4.8 KiB setup noarch 2.15.0-25.fc43 fedora 725.0 KiB sqlite-libs x86_64 3.50.0-1.fc43 fedora 1.5 MiB systemd-libs x86_64 257.6-1.fc43 fedora 2.2 MiB systemd-standalone-sysusers x86_64 257.6-1.fc43 fedora 277.3 KiB tpm2-tss x86_64 4.1.3-7.fc43 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0.2.4-1.fc43 fedora 7.5 KiB util-linux-core x86_64 2.40.4-7.fc43 fedora 1.4 MiB xxhash-libs x86_64 0.8.3-2.fc42 fedora 90.2 KiB xz-libs x86_64 1:5.8.1-1.fc43 fedora 217.8 KiB zig-srpm-macros noarch 1-4.fc42 fedora 1.1 KiB zip x86_64 3.0-43.fc42 fedora 698.5 KiB zlib-ng-compat x86_64 2.2.4-2.fc43 fedora 137.6 KiB zstd x86_64 1.5.7-1.fc43 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 168 packages Total size of inbound packages is 58 MiB. Need to download 58 MiB. After this operation, 197 MiB extra will be used (install 197 MiB, remove 0 B). [ 1/168] bzip2-0:1.0.8-20.fc42.x86_64 100% | 777.1 KiB/s | 52.1 KiB | 00m00s [ 2/168] cpio-0:2.15-2.fc41.x86_64 100% | 3.3 MiB/s | 291.8 KiB | 00m00s [ 3/168] coreutils-0:9.7-3.fc43.x86_64 100% | 6.3 MiB/s | 1.1 MiB | 00m00s [ 4/168] diffutils-0:3.12-2.fc43.x86_6 100% | 9.1 MiB/s | 392.7 KiB | 00m00s [ 5/168] bash-0:5.2.37-3.fc43.x86_64 100% | 8.9 MiB/s | 1.8 MiB | 00m00s [ 6/168] glibc-minimal-langpack-0:2.41 100% | 1.9 MiB/s | 26.7 KiB | 00m00s [ 7/168] fedora-release-common-0:43-0. 100% | 528.6 KiB/s | 25.9 KiB | 00m00s [ 8/168] grep-0:3.12-1.fc43.x86_64 100% | 16.2 MiB/s | 299.5 KiB | 00m00s [ 9/168] findutils-1:4.10.0-5.fc42.x86 100% | 11.7 MiB/s | 551.5 KiB | 00m00s [ 10/168] gzip-0:1.13-3.fc42.x86_64 100% | 10.4 MiB/s | 170.4 KiB | 00m00s [ 11/168] info-0:7.2-3.fc42.x86_64 100% | 12.0 MiB/s | 183.8 KiB | 00m00s [ 12/168] patch-0:2.8-1.fc43.x86_64 100% | 6.9 MiB/s | 113.7 KiB | 00m00s [ 13/168] redhat-rpm-config-0:343-6.fc4 100% | 5.2 MiB/s | 79.4 KiB | 00m00s [ 14/168] rpm-build-0:5.99.90-5.fc43.x8 100% | 8.7 MiB/s | 133.2 KiB | 00m00s [ 15/168] sed-0:4.9-4.fc42.x86_64 100% | 14.8 MiB/s | 317.3 KiB | 00m00s [ 16/168] tar-2:1.35-5.fc42.x86_64 100% | 13.6 MiB/s | 862.5 KiB | 00m00s [ 17/168] shadow-utils-2:4.17.4-1.fc43. 100% | 19.2 MiB/s | 1.3 MiB | 00m00s [ 18/168] unzip-0:6.0-66.fc42.x86_64 100% | 3.1 MiB/s | 184.6 KiB | 00m00s [ 19/168] which-0:2.23-1.fc42.x86_64 100% | 2.9 MiB/s | 41.7 KiB | 00m00s [ 20/168] xz-1:5.8.1-1.fc43.x86_64 100% | 28.0 MiB/s | 572.5 KiB | 00m00s [ 21/168] gawk-0:5.3.2-1.fc43.x86_64 100% | 31.2 MiB/s | 1.1 MiB | 00m00s [ 22/168] util-linux-0:2.40.4-7.fc43.x8 100% | 23.1 MiB/s | 1.2 MiB | 00m00s [ 23/168] filesystem-0:3.18-44.fc43.x86 100% | 26.7 MiB/s | 1.3 MiB | 00m00s [ 24/168] ncurses-libs-0:6.5-5.20250125 100% | 17.2 MiB/s | 335.0 KiB | 00m00s [ 25/168] coreutils-common-0:9.7-3.fc43 100% | 55.3 MiB/s | 2.1 MiB | 00m00s [ 26/168] gmp-1:6.3.0-3.fc43.x86_64 100% | 18.5 MiB/s | 322.2 KiB | 00m00s [ 27/168] libacl-0:2.3.2-3.fc42.x86_64 100% | 1.6 MiB/s | 23.0 KiB | 00m00s [ 28/168] libattr-0:2.5.2-5.fc42.x86_64 100% | 589.1 KiB/s | 17.1 KiB | 00m00s [ 29/168] libcap-0:2.76-1.fc43.x86_64 100% | 5.7 MiB/s | 86.9 KiB | 00m00s [ 30/168] bzip2-libs-0:1.0.8-20.fc42.x8 100% | 262.5 KiB/s | 43.6 KiB | 00m00s [ 31/168] openssl-libs-1:3.5.0-3.fc43.x 100% | 31.4 MiB/s | 2.6 MiB | 00m00s [ 32/168] glibc-0:2.41.9000-15.fc43.x86 100% | 9.1 MiB/s | 2.2 MiB | 00m00s [ 33/168] fedora-repos-0:43-0.2.noarch 100% | 659.2 KiB/s | 9.2 KiB | 00m00s [ 34/168] systemd-libs-0:257.6-1.fc43.x 100% | 11.2 MiB/s | 789.6 KiB | 00m00s [ 35/168] glibc-common-0:2.41.9000-15.f 100% | 14.6 MiB/s | 313.3 KiB | 00m00s [ 36/168] pcre2-0:10.45-1.fc43.x86_64 100% | 16.0 MiB/s | 262.8 KiB | 00m00s [ 37/168] ed-0:1.21-2.fc42.x86_64 100% | 4.0 MiB/s | 82.0 KiB | 00m00s [ 38/168] ansible-srpm-macros-0:1-17.1. 100% | 1.0 MiB/s | 20.3 KiB | 00m00s [ 39/168] build-reproducibility-srpm-ma 100% | 834.5 KiB/s | 11.7 KiB | 00m00s [ 40/168] efi-srpm-macros-0:6-3.fc43.no 100% | 1.6 MiB/s | 22.5 KiB | 00m00s [ 41/168] dwz-0:0.15-9.fc42.x86_64 100% | 8.8 MiB/s | 135.7 KiB | 00m00s [ 42/168] filesystem-srpm-macros-0:3.18 100% | 1.8 MiB/s | 26.0 KiB | 00m00s [ 43/168] fonts-srpm-macros-1:2.0.5-22. 100% | 1.9 MiB/s | 27.2 KiB | 00m00s [ 44/168] forge-srpm-macros-0:0.4.0-2.f 100% | 1.4 MiB/s | 19.9 KiB | 00m00s [ 45/168] fpc-srpm-macros-0:1.3-14.fc42 100% | 572.8 KiB/s | 8.0 KiB | 00m00s [ 46/168] ghc-srpm-macros-0:1.9.2-2.fc4 100% | 654.0 KiB/s | 9.2 KiB | 00m00s [ 47/168] gnat-srpm-macros-0:6-7.fc42.n 100% | 615.1 KiB/s | 8.6 KiB | 00m00s [ 48/168] go-srpm-macros-0:3.6.0-7.fc43 100% | 1.9 MiB/s | 27.6 KiB | 00m00s [ 49/168] java-srpm-macros-0:1-3.fc43.n 100% | 508.6 KiB/s | 7.1 KiB | 00m00s [ 50/168] kernel-srpm-macros-0:1.0-25.f 100% | 705.1 KiB/s | 9.9 KiB | 00m00s [ 51/168] lua-srpm-macros-0:1-15.fc42.n 100% | 636.9 KiB/s | 8.9 KiB | 00m00s [ 52/168] ocaml-srpm-macros-0:10-4.fc42 100% | 657.5 KiB/s | 9.2 KiB | 00m00s [ 53/168] openblas-srpm-macros-0:2-19.f 100% | 554.7 KiB/s | 7.8 KiB | 00m00s [ 54/168] package-notes-srpm-macros-0:0 100% | 661.4 KiB/s | 9.3 KiB | 00m00s [ 55/168] perl-srpm-macros-0:1-57.fc42. 100% | 607.6 KiB/s | 8.5 KiB | 00m00s [ 56/168] python-srpm-macros-0:3.13-5.f 100% | 1.6 MiB/s | 23.2 KiB | 00m00s [ 57/168] qt5-srpm-macros-0:5.15.17-1.f 100% | 622.8 KiB/s | 8.7 KiB | 00m00s [ 58/168] qt6-srpm-macros-0:6.9.0-2.fc4 100% | 670.2 KiB/s | 9.4 KiB | 00m00s [ 59/168] rust-srpm-macros-0:26.3-4.fc4 100% | 780.3 KiB/s | 11.7 KiB | 00m00s [ 60/168] rpm-0:5.99.90-5.fc43.x86_64 100% | 25.8 MiB/s | 555.8 KiB | 00m00s [ 61/168] tree-sitter-srpm-macros-0:0.2 100% | 889.5 KiB/s | 12.5 KiB | 00m00s [ 62/168] zig-srpm-macros-0:1-4.fc42.no 100% | 588.9 KiB/s | 8.2 KiB | 00m00s [ 63/168] zip-0:3.0-43.fc42.x86_64 100% | 16.1 MiB/s | 263.5 KiB | 00m00s [ 64/168] debugedit-0:5.1-6.fc43.x86_64 100% | 5.5 MiB/s | 78.7 KiB | 00m00s [ 65/168] elfutils-0:0.193-2.fc43.x86_6 100% | 27.9 MiB/s | 571.5 KiB | 00m00s [ 66/168] elfutils-libelf-0:0.193-2.fc4 100% | 10.2 MiB/s | 207.9 KiB | 00m00s [ 67/168] libarchive-0:3.8.1-1.fc43.x86 100% | 21.7 MiB/s | 421.4 KiB | 00m00s [ 68/168] libgcc-0:15.1.1-2.fc43.x86_64 100% | 8.3 MiB/s | 127.5 KiB | 00m00s [ 69/168] popt-0:1.19-8.fc42.x86_64 100% | 3.8 MiB/s | 66.0 KiB | 00m00s [ 70/168] libstdc++-0:15.1.1-2.fc43.x86 100% | 37.1 MiB/s | 912.8 KiB | 00m00s [ 71/168] readline-0:8.2-13.fc43.x86_64 100% | 10.9 MiB/s | 212.9 KiB | 00m00s [ 72/168] rpm-build-libs-0:5.99.90-5.fc 100% | 8.3 MiB/s | 127.4 KiB | 00m00s [ 73/168] rpm-libs-0:5.99.90-5.fc43.x86 100% | 19.5 MiB/s | 399.9 KiB | 00m00s [ 74/168] libeconf-0:0.7.6-1.fc43.x86_6 100% | 2.5 MiB/s | 35.2 KiB | 00m00s [ 75/168] libxcrypt-0:4.4.38-7.fc43.x86 100% | 8.3 MiB/s | 127.2 KiB | 00m00s [ 76/168] audit-libs-0:4.0.4-2.fc43.x86 100% | 1.8 MiB/s | 129.4 KiB | 00m00s [ 77/168] zstd-0:1.5.7-1.fc43.x86_64 100% | 5.9 MiB/s | 485.8 KiB | 00m00s [ 78/168] setup-0:2.15.0-25.fc43.noarch 100% | 9.6 MiB/s | 157.6 KiB | 00m00s [ 79/168] xz-libs-1:5.8.1-1.fc43.x86_64 100% | 6.9 MiB/s | 113.0 KiB | 00m00s [ 80/168] libblkid-0:2.40.4-7.fc43.x86_ 100% | 7.0 MiB/s | 122.5 KiB | 00m00s [ 81/168] mpfr-0:4.2.2-1.fc43.x86_64 100% | 17.8 MiB/s | 346.7 KiB | 00m00s [ 82/168] libcap-ng-0:0.8.5-4.fc42.x86_ 100% | 2.2 MiB/s | 32.2 KiB | 00m00s [ 83/168] libfdisk-0:2.40.4-7.fc43.x86_ 100% | 6.2 MiB/s | 158.2 KiB | 00m00s [ 84/168] libmount-0:2.40.4-7.fc43.x86_ 100% | 10.1 MiB/s | 155.0 KiB | 00m00s [ 85/168] pam-libs-0:1.7.0-4.fc42.x86_6 100% | 455.6 KiB/s | 58.3 KiB | 00m00s [ 86/168] util-linux-core-0:2.40.4-7.fc 100% | 27.2 MiB/s | 529.5 KiB | 00m00s [ 87/168] libsmartcols-0:2.40.4-7.fc43. 100% | 1.3 MiB/s | 81.2 KiB | 00m00s [ 88/168] libuuid-0:2.40.4-7.fc43.x86_6 100% | 436.8 KiB/s | 25.3 KiB | 00m00s [ 89/168] zlib-ng-compat-0:2.2.4-2.fc43 100% | 4.8 MiB/s | 79.1 KiB | 00m00s [ 90/168] ncurses-base-0:6.5-5.20250125 100% | 4.8 MiB/s | 88.1 KiB | 00m00s [ 91/168] crypto-policies-0:20250602-1. 100% | 3.4 MiB/s | 97.7 KiB | 00m00s [ 92/168] glibc-gconv-extra-0:2.41.9000 100% | 30.8 MiB/s | 1.6 MiB | 00m00s [ 93/168] ca-certificates-0:2024.2.69_v 100% | 21.5 MiB/s | 945.0 KiB | 00m00s [ 94/168] fedora-gpg-keys-0:43-0.2.noar 100% | 8.9 MiB/s | 136.6 KiB | 00m00s [ 95/168] fedora-repos-rawhide-0:43-0.2 100% | 628.8 KiB/s | 8.8 KiB | 00m00s [ 96/168] pcre2-syntax-0:10.45-1.fc43.n 100% | 6.6 MiB/s | 161.7 KiB | 00m00s [ 97/168] curl-0:8.14.0-1.fc43.x86_64 100% | 12.7 MiB/s | 234.0 KiB | 00m00s [ 98/168] add-determinism-0:0.6.0-1.fc4 100% | 35.9 MiB/s | 918.3 KiB | 00m00s [ 99/168] elfutils-libs-0:0.193-2.fc43. 100% | 15.5 MiB/s | 270.2 KiB | 00m00s [100/168] elfutils-debuginfod-client-0: 100% | 3.3 MiB/s | 47.0 KiB | 00m00s [101/168] libzstd-0:1.5.7-1.fc43.x86_64 100% | 18.1 MiB/s | 314.8 KiB | 00m00s [102/168] lz4-libs-0:1.10.0-2.fc42.x86_ 100% | 4.8 MiB/s | 78.1 KiB | 00m00s [103/168] libxml2-0:2.12.10-1.fc43.x86_ 100% | 29.0 MiB/s | 682.9 KiB | 00m00s [104/168] libgomp-0:15.1.1-2.fc43.x86_6 100% | 19.8 MiB/s | 365.2 KiB | 00m00s [105/168] lua-libs-0:5.4.7-3.fc43.x86_6 100% | 8.5 MiB/s | 130.4 KiB | 00m00s [106/168] rpm-sign-libs-0:5.99.90-5.fc4 100% | 2.0 MiB/s | 29.2 KiB | 00m00s [107/168] rpm-sequoia-0:1.8.0-1.fc43.x8 100% | 36.7 MiB/s | 938.8 KiB | 00m00s [108/168] elfutils-default-yama-scope-0 100% | 572.1 KiB/s | 12.6 KiB | 00m00s [109/168] sqlite-libs-0:3.50.0-1.fc43.x 100% | 29.7 MiB/s | 761.3 KiB | 00m00s [110/168] json-c-0:0.18-2.fc42.x86_64 100% | 3.1 MiB/s | 44.9 KiB | 00m00s [111/168] ima-evm-utils-libs-0:1.6.2-5. 100% | 1.9 MiB/s | 29.5 KiB | 00m00s [112/168] libfsverity-0:1.6-2.fc42.x86_ 100% | 894.4 KiB/s | 18.8 KiB | 00m00s [113/168] gpgverify-0:2.1-3.fc43.noarch 100% | 632.5 KiB/s | 10.8 KiB | 00m00s [114/168] gnupg2-0:2.4.8-2.fc43.x86_64 100% | 43.3 MiB/s | 1.6 MiB | 00m00s [115/168] gnupg2-dirmngr-0:2.4.8-2.fc43 100% | 14.1 MiB/s | 274.8 KiB | 00m00s [116/168] gnupg2-gpg-agent-0:2.4.8-2.fc 100% | 13.3 MiB/s | 273.0 KiB | 00m00s [117/168] gnupg2-gpgconf-0:2.4.8-2.fc43 100% | 6.2 MiB/s | 115.2 KiB | 00m00s [118/168] gnupg2-keyboxd-0:2.4.8-2.fc43 100% | 6.2 MiB/s | 94.8 KiB | 00m00s [119/168] libassuan-0:2.5.7-3.fc42.x86_ 100% | 3.1 MiB/s | 67.6 KiB | 00m00s [120/168] gnupg2-verify-0:2.4.8-2.fc43. 100% | 7.6 MiB/s | 171.3 KiB | 00m00s [121/168] libgcrypt-0:1.11.1-1.fc43.x86 100% | 18.2 MiB/s | 596.1 KiB | 00m00s [122/168] npth-0:1.8-2.fc42.x86_64 100% | 1.0 MiB/s | 25.8 KiB | 00m00s [123/168] libgpg-error-0:1.55-1.fc43.x8 100% | 9.2 MiB/s | 244.1 KiB | 00m00s [124/168] tpm2-tss-0:4.1.3-7.fc43.x86_6 100% | 20.7 MiB/s | 423.4 KiB | 00m00s [125/168] libksba-0:1.6.7-3.fc42.x86_64 100% | 7.2 MiB/s | 162.0 KiB | 00m00s [126/168] gnutls-0:3.8.9-5.fc43.x86_64 100% | 18.4 MiB/s | 1.2 MiB | 00m00s [127/168] libusb1-0:1.0.28-2.fc43.x86_6 100% | 1.5 MiB/s | 79.3 KiB | 00m00s [128/168] libidn2-0:2.3.8-1.fc43.x86_64 100% | 10.7 MiB/s | 174.8 KiB | 00m00s [129/168] libtasn1-0:4.20.0-1.fc43.x86_ 100% | 5.2 MiB/s | 75.0 KiB | 00m00s [130/168] openldap-0:2.6.9-5.fc43.x86_6 100% | 3.1 MiB/s | 258.6 KiB | 00m00s [131/168] libunistring-0:1.1-9.fc42.x86 100% | 25.2 MiB/s | 542.5 KiB | 00m00s [132/168] nettle-0:3.10.1-1.fc43.x86_64 100% | 16.6 MiB/s | 424.6 KiB | 00m00s [133/168] cyrus-sasl-lib-0:2.1.28-30.fc 100% | 11.4 MiB/s | 793.5 KiB | 00m00s [134/168] libtool-ltdl-0:2.5.4-4.fc42.x 100% | 2.4 MiB/s | 36.2 KiB | 00m00s [135/168] libevent-0:2.1.12-15.fc42.x86 100% | 3.3 MiB/s | 260.2 KiB | 00m00s [136/168] libffi-0:3.4.8-1.fc43.x86_64 100% | 2.6 MiB/s | 40.5 KiB | 00m00s [137/168] gdbm-libs-1:1.23-9.fc42.x86_6 100% | 1.5 MiB/s | 57.0 KiB | 00m00s [138/168] p11-kit-0:0.25.5-8.fc43.x86_6 100% | 3.4 MiB/s | 488.2 KiB | 00m00s [139/168] libselinux-0:3.8-3.fc43.x86_6 100% | 2.2 MiB/s | 97.2 KiB | 00m00s [140/168] libsepol-0:3.8-1.fc42.x86_64 100% | 12.6 MiB/s | 348.9 KiB | 00m00s [141/168] jansson-0:2.14-2.fc42.x86_64 100% | 3.0 MiB/s | 45.7 KiB | 00m00s [142/168] alternatives-0:1.33-1.fc43.x8 100% | 1.4 MiB/s | 40.5 KiB | 00m00s [143/168] libsemanage-0:3.8.1-3.fc43.x8 100% | 6.0 MiB/s | 123.8 KiB | 00m00s [144/168] file-libs-0:5.46-4.fc43.x86_6 100% | 23.1 MiB/s | 850.2 KiB | 00m00s [145/168] file-0:5.46-4.fc43.x86_64 100% | 2.3 MiB/s | 49.2 KiB | 00m00s [146/168] pkgconf-pkg-config-0:2.3.0-2. 100% | 708.9 KiB/s | 9.9 KiB | 00m00s [147/168] pkgconf-m4-0:2.3.0-2.fc42.noa 100% | 1.0 MiB/s | 14.2 KiB | 00m00s [148/168] pkgconf-0:2.3.0-2.fc42.x86_64 100% | 1.4 MiB/s | 44.9 KiB | 00m00s [149/168] pyproject-srpm-macros-0:1.18. 100% | 1.4 MiB/s | 14.5 KiB | 00m00s [150/168] libpkgconf-0:2.3.0-2.fc42.x86 100% | 299.8 KiB/s | 38.4 KiB | 00m00s [151/168] fedora-release-0:43-0.16.noar 100% | 1.0 MiB/s | 14.9 KiB | 00m00s [152/168] systemd-standalone-sysusers-0 100% | 7.3 MiB/s | 134.4 KiB | 00m00s [153/168] p11-kit-trust-0:0.25.5-8.fc43 100% | 833.0 KiB/s | 132.4 KiB | 00m00s [154/168] xxhash-libs-0:0.8.3-2.fc42.x8 100% | 1.5 MiB/s | 39.1 KiB | 00m00s [155/168] binutils-0:2.44-3.fc43.x86_64 100% | 18.0 MiB/s | 5.8 MiB | 00m00s [156/168] fedora-release-identity-basic 100% | 710.5 KiB/s | 15.6 KiB | 00m00s [157/168] libcurl-0:8.14.0-1.fc43.x86_6 100% | 12.2 MiB/s | 399.7 KiB | 00m00s [158/168] libnghttp2-0:1.65.0-1.fc43.x8 100% | 4.7 MiB/s | 72.6 KiB | 00m00s [159/168] libpsl-0:0.21.5-5.fc42.x86_64 100% | 3.3 MiB/s | 64.0 KiB | 00m00s [160/168] libssh-0:0.11.1-4.fc42.x86_64 100% | 12.0 MiB/s | 233.3 KiB | 00m00s [161/168] gdb-minimal-0:16.3-1.fc43.x86 100% | 28.3 MiB/s | 4.4 MiB | 00m00s [162/168] keyutils-libs-0:1.6.3-5.fc42. 100% | 2.2 MiB/s | 31.5 KiB | 00m00s [163/168] libcom_err-0:1.47.2-3.fc42.x8 100% | 1.9 MiB/s | 26.9 KiB | 00m00s [164/168] libverto-0:0.3.2-10.fc42.x86_ 100% | 1.1 MiB/s | 20.8 KiB | 00m00s [165/168] libssh-config-0:0.11.1-4.fc42 100% | 643.1 KiB/s | 9.0 KiB | 00m00s [166/168] publicsuffix-list-dafsa-0:202 100% | 2.0 MiB/s | 58.8 KiB | 00m00s [167/168] libbrotli-0:1.1.0-7.fc43.x86_ 100% | 15.1 MiB/s | 339.6 KiB | 00m00s [168/168] krb5-libs-0:1.21.3-5.fc42.x86 100% | 3.8 MiB/s | 764.7 KiB | 00m00s -------------------------------------------------------------------------------- [168/168] Total 100% | 27.5 MiB/s | 58.4 MiB | 00m02s Running transaction Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. [ 1/170] Verify package files 100% | 1.4 KiB/s | 168.0 B | 00m00s >>> Running pre-transaction scriptlet: filesystem-0:3.18-44.fc43.x86_64 >>> Finished pre-transaction scriptlet: filesystem-0:3.18-44.fc43.x86_64 >>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1748989340.287934/root/var/cache/d [ 2/170] Prepare transaction 100% | 1.9 KiB/s | 168.0 B | 00m00s [ 3/170] Installing libgcc-0:15.1.1-2. 100% | 87.3 MiB/s | 268.3 KiB | 00m00s [ 4/170] Installing libssh-config-0:0. 100% | 265.6 KiB/s | 816.0 B | 00m00s [ 5/170] Installing publicsuffix-list- 100% | 67.6 MiB/s | 69.2 KiB | 00m00s [ 6/170] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0 B | 00m00s [ 7/170] Installing fedora-gpg-keys-0: 100% | 13.2 MiB/s | 175.9 KiB | 00m00s [ 8/170] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 9/170] Installing fedora-repos-0:43- 100% | 5.6 MiB/s | 5.7 KiB | 00m00s [ 10/170] Installing fedora-release-com 100% | 12.1 MiB/s | 24.7 KiB | 00m00s [ 11/170] Installing fedora-release-0:4 100% | 4.7 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-25.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-25.fc43.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 12/170] Installing setup-0:2.15.0-25. 100% | 32.4 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/170] Installing filesystem-0:3.18- 100% | 1.3 MiB/s | 212.5 KiB | 00m00s [ 14/170] Installing pkgconf-m4-0:2.3.0 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [ 15/170] Installing pcre2-syntax-0:10. 100% | 135.0 MiB/s | 276.4 KiB | 00m00s [ 16/170] Installing ncurses-base-0:6.5 100% | 31.3 MiB/s | 352.2 KiB | 00m00s [ 17/170] Installing bash-0:5.2.37-3.fc 100% | 136.3 MiB/s | 8.2 MiB | 00m00s [ 18/170] Installing glibc-common-0:2.4 100% | 40.8 MiB/s | 1.0 MiB | 00m00s [ 19/170] Installing glibc-gconv-extra- 100% | 114.3 MiB/s | 7.3 MiB | 00m00s [ 20/170] Installing glibc-0:2.41.9000- 100% | 98.2 MiB/s | 6.7 MiB | 00m00s [ 21/170] Installing ncurses-libs-0:6.5 100% | 155.1 MiB/s | 952.8 KiB | 00m00s [ 22/170] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 23/170] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB | 00m00s [ 24/170] Installing bzip2-libs-0:1.0.8 100% | 83.7 MiB/s | 85.7 KiB | 00m00s [ 25/170] Installing libgpg-error-0:1.5 100% | 42.8 MiB/s | 921.1 KiB | 00m00s [ 26/170] Installing libstdc++-0:15.1.1 100% | 166.8 MiB/s | 2.8 MiB | 00m00s [ 27/170] Installing xz-libs-1:5.8.1-1. 100% | 106.9 MiB/s | 218.9 KiB | 00m00s [ 28/170] Installing libassuan-0:2.5.7- 100% | 41.4 MiB/s | 169.6 KiB | 00m00s [ 29/170] Installing libgcrypt-0:1.11.1 100% | 262.5 MiB/s | 1.6 MiB | 00m00s [ 30/170] Installing readline-0:8.2-13. 100% | 95.1 MiB/s | 487.1 KiB | 00m00s [ 31/170] Installing gmp-1:6.3.0-3.fc43 100% | 200.6 MiB/s | 821.5 KiB | 00m00s [ 32/170] Installing libuuid-0:2.40.4-7 100% | 37.5 MiB/s | 38.4 KiB | 00m00s [ 33/170] Installing popt-0:1.19-8.fc42 100% | 27.2 MiB/s | 139.4 KiB | 00m00s [ 34/170] Installing npth-0:1.8-2.fc42. 100% | 16.5 MiB/s | 50.7 KiB | 00m00s [ 35/170] Installing libblkid-0:2.40.4- 100% | 128.6 MiB/s | 263.4 KiB | 00m00s [ 36/170] Installing libxcrypt-0:4.4.38 100% | 140.2 MiB/s | 287.2 KiB | 00m00s [ 37/170] Installing libzstd-0:1.5.7-1. 100% | 6.4 MiB/s | 809.1 KiB | 00m00s [ 38/170] Installing elfutils-libelf-0: 100% | 233.3 MiB/s | 1.2 MiB | 00m00s [ 39/170] Installing gnupg2-gpgconf-0:2 100% | 16.4 MiB/s | 252.1 KiB | 00m00s [ 40/170] Installing libattr-0:2.5.2-5. 100% | 6.9 MiB/s | 28.1 KiB | 00m00s [ 41/170] Installing libacl-0:2.3.2-3.f 100% | 38.2 MiB/s | 39.2 KiB | 00m00s [ 42/170] Installing sqlite-libs-0:3.50 100% | 252.7 MiB/s | 1.5 MiB | 00m00s [ 43/170] Installing libtasn1-0:4.20.0- 100% | 43.5 MiB/s | 178.1 KiB | 00m00s [ 44/170] Installing libunistring-0:1.1 100% | 115.1 MiB/s | 1.7 MiB | 00m00s [ 45/170] Installing libidn2-0:2.3.8-1. 100% | 23.7 MiB/s | 558.7 KiB | 00m00s [ 46/170] Installing crypto-policies-0: 100% | 13.7 MiB/s | 167.7 KiB | 00m00s [ 47/170] Installing dwz-0:0.15-9.fc42. 100% | 16.8 MiB/s | 292.4 KiB | 00m00s [ 48/170] Installing mpfr-0:4.2.2-1.fc4 100% | 115.8 MiB/s | 830.4 KiB | 00m00s [ 49/170] Installing gawk-0:5.3.2-1.fc4 100% | 67.3 MiB/s | 1.8 MiB | 00m00s [ 50/170] Installing libksba-0:1.6.7-3. 100% | 131.9 MiB/s | 405.1 KiB | 00m00s [ 51/170] Installing unzip-0:6.0-66.fc4 100% | 20.2 MiB/s | 393.8 KiB | 00m00s [ 52/170] Installing file-libs-0:5.46-4 100% | 167.0 MiB/s | 11.9 MiB | 00m00s [ 53/170] Installing file-0:5.46-4.fc43 100% | 6.6 MiB/s | 101.7 KiB | 00m00s [ 54/170] Installing pcre2-0:10.45-1.fc 100% | 170.7 MiB/s | 699.1 KiB | 00m00s [ 55/170] Installing grep-0:3.12-1.fc43 100% | 41.8 MiB/s | 1.0 MiB | 00m00s [ 56/170] Installing xz-1:5.8.1-1.fc43. 100% | 9.4 MiB/s | 1.3 MiB | 00m00s [ 57/170] Installing libeconf-0:0.7.6-1 100% | 32.3 MiB/s | 66.2 KiB | 00m00s [ 58/170] Installing libcap-ng-0:0.8.5- 100% | 36.5 MiB/s | 74.8 KiB | 00m00s [ 59/170] Installing audit-libs-0:4.0.4 100% | 115.0 MiB/s | 353.3 KiB | 00m00s [ 60/170] Installing pam-libs-0:1.7.0-4 100% | 5.7 MiB/s | 129.1 KiB | 00m00s [ 61/170] Installing libcap-0:2.76-1.fc 100% | 11.6 MiB/s | 214.3 KiB | 00m00s [ 62/170] Installing systemd-libs-0:257 100% | 117.5 MiB/s | 2.2 MiB | 00m00s [ 63/170] Installing libsmartcols-0:2.4 100% | 88.6 MiB/s | 181.5 KiB | 00m00s [ 64/170] Installing lz4-libs-0:1.10.0- 100% | 77.4 MiB/s | 158.5 KiB | 00m00s [ 65/170] Installing lua-libs-0:5.4.7-3 100% | 22.6 MiB/s | 278.1 KiB | 00m00s [ 66/170] Installing json-c-0:0.18-2.fc 100% | 43.0 MiB/s | 88.0 KiB | 00m00s [ 67/170] Installing libffi-0:3.4.8-1.f 100% | 41.2 MiB/s | 84.3 KiB | 00m00s [ 68/170] Installing p11-kit-0:0.25.5-8 100% | 42.8 MiB/s | 2.2 MiB | 00m00s [ 69/170] Installing libsepol-0:3.8-1.f 100% | 89.7 MiB/s | 827.0 KiB | 00m00s [ 70/170] Installing libselinux-0:3.8-3 100% | 94.9 MiB/s | 194.3 KiB | 00m00s [ 71/170] Installing findutils-1:4.10.0 100% | 48.0 MiB/s | 1.9 MiB | 00m00s [ 72/170] Installing sed-0:4.9-4.fc42.x 100% | 23.5 MiB/s | 865.5 KiB | 00m00s [ 73/170] Installing libmount-0:2.40.4- 100% | 116.3 MiB/s | 357.4 KiB | 00m00s [ 74/170] Installing alternatives-0:1.3 100% | 4.2 MiB/s | 63.8 KiB | 00m00s [ 75/170] Installing p11-kit-trust-0:0. 100% | 11.1 MiB/s | 397.1 KiB | 00m00s [ 76/170] Installing util-linux-core-0: 100% | 40.8 MiB/s | 1.4 MiB | 00m00s [ 77/170] Installing tar-2:1.35-5.fc42. 100% | 52.0 MiB/s | 3.0 MiB | 00m00s [ 78/170] Installing libsemanage-0:3.8. 100% | 99.7 MiB/s | 306.2 KiB | 00m00s [ 79/170] Installing systemd-standalone 100% | 18.1 MiB/s | 278.0 KiB | 00m00s [ 80/170] Installing zstd-0:1.5.7-1.fc4 100% | 63.3 MiB/s | 1.7 MiB | 00m00s [ 81/170] Installing libusb1-0:1.0.28-2 100% | 28.1 MiB/s | 172.7 KiB | 00m00s [ 82/170] Installing zip-0:3.0-43.fc42. 100% | 38.1 MiB/s | 702.4 KiB | 00m00s [ 83/170] Installing gnupg2-keyboxd-0:2 100% | 11.6 MiB/s | 202.7 KiB | 00m00s [ 84/170] Installing libpsl-0:0.21.5-5. 100% | 37.9 MiB/s | 77.5 KiB | 00m00s [ 85/170] Installing libfdisk-0:2.40.4- 100% | 22.8 MiB/s | 373.5 KiB | 00m00s [ 86/170] Installing gnupg2-verify-0:2. 100% | 19.0 MiB/s | 349.9 KiB | 00m00s [ 87/170] Installing nettle-0:3.10.1-1. 100% | 48.4 MiB/s | 793.6 KiB | 00m00s [ 88/170] Installing gnutls-0:3.8.9-5.f 100% | 89.3 MiB/s | 3.6 MiB | 00m00s [ 89/170] Installing libxml2-0:2.12.10- 100% | 56.6 MiB/s | 1.7 MiB | 00m00s [ 90/170] Installing bzip2-0:1.0.8-20.f 100% | 4.8 MiB/s | 103.8 KiB | 00m00s [ 91/170] Installing add-determinism-0: 100% | 25.2 MiB/s | 2.5 MiB | 00m00s [ 92/170] Installing build-reproducibil 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [ 93/170] Installing cpio-0:2.15-2.fc41 100% | 37.9 MiB/s | 1.1 MiB | 00m00s [ 94/170] Installing diffutils-0:3.12-2 100% | 47.3 MiB/s | 1.6 MiB | 00m00s [ 95/170] Installing ed-0:1.21-2.fc42.x 100% | 7.6 MiB/s | 148.8 KiB | 00m00s [ 96/170] Installing patch-0:2.8-1.fc43 100% | 11.7 MiB/s | 228.3 KiB | 00m00s [ 97/170] Installing libgomp-0:15.1.1-2 100% | 7.3 MiB/s | 540.5 KiB | 00m00s [ 98/170] Installing libtool-ltdl-0:2.5 100% | 34.8 MiB/s | 71.2 KiB | 00m00s [ 99/170] Installing gdbm-libs-1:1.23-9 100% | 64.2 MiB/s | 131.6 KiB | 00m00s [100/170] Installing cyrus-sasl-lib-0:2 100% | 64.0 MiB/s | 2.3 MiB | 00m00s [101/170] Installing jansson-0:2.14-2.f 100% | 46.1 MiB/s | 94.4 KiB | 00m00s [102/170] Installing libpkgconf-0:2.3.0 100% | 77.4 MiB/s | 79.2 KiB | 00m00s [103/170] Installing pkgconf-0:2.3.0-2. 100% | 5.2 MiB/s | 91.0 KiB | 00m00s [104/170] Installing pkgconf-pkg-config 100% | 136.4 KiB/s | 1.8 KiB | 00m00s [105/170] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [106/170] Installing libnghttp2-0:1.65. 100% | 159.5 MiB/s | 163.3 KiB | 00m00s [107/170] Installing keyutils-libs-0:1. 100% | 58.3 MiB/s | 59.7 KiB | 00m00s [108/170] Installing libcom_err-0:1.47. 100% | 66.6 MiB/s | 68.2 KiB | 00m00s [109/170] Installing libverto-0:0.3.2-1 100% | 26.6 MiB/s | 27.2 KiB | 00m00s [110/170] Installing libbrotli-0:1.1.0- 100% | 58.3 MiB/s | 835.6 KiB | 00m00s [111/170] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [112/170] Installing elfutils-default-y 100% | 136.2 KiB/s | 2.0 KiB | 00m00s [113/170] Installing elfutils-libs-0:0. 100% | 167.3 MiB/s | 685.2 KiB | 00m00s [114/170] Installing rust-srpm-macros-0 100% | 1.8 MiB/s | 5.6 KiB | 00m00s [115/170] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [116/170] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [117/170] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [118/170] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [119/170] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [120/170] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [121/170] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [122/170] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [123/170] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [124/170] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [125/170] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [126/170] Installing coreutils-common-0 100% | 91.1 MiB/s | 11.3 MiB | 00m00s [127/170] Installing openssl-libs-1:3.5 100% | 96.6 MiB/s | 8.9 MiB | 00m00s [128/170] Installing coreutils-0:9.7-3. 100% | 60.5 MiB/s | 5.4 MiB | 00m00s [129/170] Installing ca-certificates-0: 100% | 970.2 KiB/s | 2.4 MiB | 00m02s [130/170] Installing libarchive-0:3.8.1 100% | 155.1 MiB/s | 953.1 KiB | 00m00s [131/170] Installing krb5-libs-0:1.21.3 100% | 71.9 MiB/s | 2.3 MiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-7.fc43.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-7.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [132/170] Installing tpm2-tss-0:4.1.3-7 100% | 112.0 MiB/s | 1.6 MiB | 00m00s [133/170] Installing ima-evm-utils-libs 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [134/170] Installing gnupg2-gpg-agent-0 100% | 18.8 MiB/s | 675.4 KiB | 00m00s [135/170] Installing libssh-0:0.11.1-4. 100% | 138.6 MiB/s | 567.5 KiB | 00m00s [136/170] Installing gzip-0:1.13-3.fc42 100% | 21.6 MiB/s | 398.4 KiB | 00m00s [137/170] Installing rpm-sequoia-0:1.8. 100% | 250.4 MiB/s | 2.5 MiB | 00m00s [138/170] Installing rpm-libs-0:5.99.90 100% | 181.9 MiB/s | 931.3 KiB | 00m00s [139/170] Installing libfsverity-0:1.6- 100% | 32.7 MiB/s | 33.5 KiB | 00m00s [140/170] Installing libevent-0:2.1.12- 100% | 177.1 MiB/s | 906.9 KiB | 00m00s [141/170] Installing openldap-0:2.6.9-5 100% | 128.7 MiB/s | 658.9 KiB | 00m00s [142/170] Installing libcurl-0:8.14.0-1 100% | 218.8 MiB/s | 896.4 KiB | 00m00s [143/170] Installing elfutils-debuginfo 100% | 5.3 MiB/s | 86.2 KiB | 00m00s [144/170] Installing elfutils-0:0.193-2 100% | 112.4 MiB/s | 2.9 MiB | 00m00s [145/170] Installing binutils-0:2.44-3. 100% | 70.8 MiB/s | 25.9 MiB | 00m00s [146/170] Installing gdb-minimal-0:16.3 100% | 131.2 MiB/s | 13.2 MiB | 00m00s [147/170] Installing debugedit-0:5.1-6. 100% | 12.7 MiB/s | 195.4 KiB | 00m00s [148/170] Installing curl-0:8.14.0-1.fc 100% | 12.5 MiB/s | 472.6 KiB | 00m00s [149/170] Installing rpm-0:5.99.90-5.fc 100% | 36.4 MiB/s | 2.5 MiB | 00m00s [150/170] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.1 KiB | 00m00s [151/170] Installing java-srpm-macros-0 100% | 0.0 B/s | 380.0 B | 00m00s [152/170] Installing lua-srpm-macros-0: 100% | 1.9 MiB/s | 1.9 KiB | 00m00s [153/170] Installing tree-sitter-srpm-m 100% | 8.4 MiB/s | 8.6 KiB | 00m00s [154/170] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [155/170] Installing gnupg2-dirmngr-0:2 100% | 16.4 MiB/s | 621.1 KiB | 00m00s [156/170] Installing gnupg2-0:2.4.8-2.f 100% | 131.0 MiB/s | 6.6 MiB | 00m00s [157/170] Installing rpm-sign-libs-0:5. 100% | 39.6 MiB/s | 40.5 KiB | 00m00s [158/170] Installing rpm-build-libs-0:5 100% | 64.7 MiB/s | 265.2 KiB | 00m00s [159/170] Installing gpgverify-0:2.1-3. 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [160/170] Installing rpm-build-0:5.99.9 100% | 15.8 MiB/s | 290.3 KiB | 00m00s [161/170] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [162/170] Installing redhat-rpm-config- 100% | 45.8 MiB/s | 187.8 KiB | 00m00s [163/170] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [164/170] Installing fonts-srpm-macros- 100% | 18.6 MiB/s | 57.0 KiB | 00m00s [165/170] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [166/170] Installing python-srpm-macros 100% | 51.8 MiB/s | 53.0 KiB | 00m00s [167/170] Installing which-0:2.23-1.fc4 100% | 5.2 MiB/s | 85.6 KiB | 00m00s [168/170] Installing util-linux-0:2.40. 100% | 49.5 MiB/s | 3.5 MiB | 00m00s [169/170] Installing shadow-utils-2:4.1 100% | 69.9 MiB/s | 4.1 MiB | 00m00s [170/170] Installing info-0:7.2-3.fc42. 100% | 109.0 KiB/s | 358.3 KiB | 00m03s Warning: skipped OpenPGP checks for 6 packages from repository: copr_base Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.6.0-1.fc43.x86_64 alternatives-1.33-1.fc43.x86_64 ansible-srpm-macros-1-17.1.fc42.noarch audit-libs-4.0.4-2.fc43.x86_64 bash-5.2.37-3.fc43.x86_64 binutils-2.44-3.fc43.x86_64 build-reproducibility-srpm-macros-0.6.0-1.fc43.noarch bzip2-1.0.8-20.fc42.x86_64 bzip2-libs-1.0.8-20.fc42.x86_64 ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch coreutils-9.7-3.fc43.x86_64 coreutils-common-9.7-3.fc43.x86_64 cpio-2.15-2.fc41.x86_64 crypto-policies-20250602-1.git9a48d06.fc43.noarch curl-8.14.0-1.fc43.x86_64 cyrus-sasl-lib-2.1.28-30.fc42.x86_64 debugedit-5.1-6.fc43.x86_64 diffutils-3.12-2.fc43.x86_64 dwz-0.15-9.fc42.x86_64 ed-1.21-2.fc42.x86_64 efi-srpm-macros-6-3.fc43.noarch elfutils-0.193-2.fc43.x86_64 elfutils-debuginfod-client-0.193-2.fc43.x86_64 elfutils-default-yama-scope-0.193-2.fc43.noarch elfutils-libelf-0.193-2.fc43.x86_64 elfutils-libs-0.193-2.fc43.x86_64 fedora-gpg-keys-43-0.2.noarch fedora-release-43-0.16.noarch fedora-release-common-43-0.16.noarch fedora-release-identity-basic-43-0.16.noarch fedora-repos-43-0.2.noarch fedora-repos-rawhide-43-0.2.noarch file-5.46-4.fc43.x86_64 file-libs-5.46-4.fc43.x86_64 filesystem-3.18-44.fc43.x86_64 filesystem-srpm-macros-3.18-44.fc43.noarch findutils-4.10.0-5.fc42.x86_64 fonts-srpm-macros-2.0.5-22.fc43.noarch forge-srpm-macros-0.4.0-2.fc42.noarch fpc-srpm-macros-1.3-14.fc42.noarch gawk-5.3.2-1.fc43.x86_64 gdb-minimal-16.3-1.fc43.x86_64 gdbm-libs-1.23-9.fc42.x86_64 ghc-srpm-macros-1.9.2-2.fc42.noarch glibc-2.41.9000-15.fc43.x86_64 glibc-common-2.41.9000-15.fc43.x86_64 glibc-gconv-extra-2.41.9000-15.fc43.x86_64 glibc-minimal-langpack-2.41.9000-15.fc43.x86_64 gmp-6.3.0-3.fc43.x86_64 gnat-srpm-macros-6-7.fc42.noarch gnupg2-2.4.8-2.fc43.x86_64 gnupg2-dirmngr-2.4.8-2.fc43.x86_64 gnupg2-gpg-agent-2.4.8-2.fc43.x86_64 gnupg2-gpgconf-2.4.8-2.fc43.x86_64 gnupg2-keyboxd-2.4.8-2.fc43.x86_64 gnupg2-verify-2.4.8-2.fc43.x86_64 gnutls-3.8.9-5.fc43.x86_64 go-srpm-macros-3.6.0-7.fc43.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-b0f4950458f69e1150c6c5edc8ac4916105ef944-65ca83d1 gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf gpgverify-2.1-3.fc43.noarch grep-3.12-1.fc43.x86_64 gzip-1.13-3.fc42.x86_64 ima-evm-utils-libs-1.6.2-5.fc43.x86_64 info-7.2-3.fc42.x86_64 jansson-2.14-2.fc42.x86_64 java-srpm-macros-1-3.fc43.noarch json-c-0.18-2.fc42.x86_64 kernel-srpm-macros-1.0-25.fc42.noarch keyutils-libs-1.6.3-5.fc42.x86_64 krb5-libs-1.21.3-5.fc42.x86_64 libacl-2.3.2-3.fc42.x86_64 libarchive-3.8.1-1.fc43.x86_64 libassuan-2.5.7-3.fc42.x86_64 libattr-2.5.2-5.fc42.x86_64 libblkid-2.40.4-7.fc43.x86_64 libbrotli-1.1.0-7.fc43.x86_64 libcap-2.76-1.fc43.x86_64 libcap-ng-0.8.5-4.fc42.x86_64 libcom_err-1.47.2-3.fc42.x86_64 libcurl-8.14.0-1.fc43.x86_64 libeconf-0.7.6-1.fc43.x86_64 libevent-2.1.12-15.fc42.x86_64 libfdisk-2.40.4-7.fc43.x86_64 libffi-3.4.8-1.fc43.x86_64 libfsverity-1.6-2.fc42.x86_64 libgcc-15.1.1-2.fc43.x86_64 libgcrypt-1.11.1-1.fc43.x86_64 libgomp-15.1.1-2.fc43.x86_64 libgpg-error-1.55-1.fc43.x86_64 libidn2-2.3.8-1.fc43.x86_64 libksba-1.6.7-3.fc42.x86_64 libmount-2.40.4-7.fc43.x86_64 libnghttp2-1.65.0-1.fc43.x86_64 libpkgconf-2.3.0-2.fc42.x86_64 libpsl-0.21.5-5.fc42.x86_64 libselinux-3.8-3.fc43.x86_64 libsemanage-3.8.1-3.fc43.x86_64 libsepol-3.8-1.fc42.x86_64 libsmartcols-2.40.4-7.fc43.x86_64 libssh-0.11.1-4.fc42.x86_64 libssh-config-0.11.1-4.fc42.noarch libstdc++-15.1.1-2.fc43.x86_64 libtasn1-4.20.0-1.fc43.x86_64 libtool-ltdl-2.5.4-4.fc42.x86_64 libunistring-1.1-9.fc42.x86_64 libusb1-1.0.28-2.fc43.x86_64 libuuid-2.40.4-7.fc43.x86_64 libverto-0.3.2-10.fc42.x86_64 libxcrypt-4.4.38-7.fc43.x86_64 libxml2-2.12.10-1.fc43.x86_64 libzstd-1.5.7-1.fc43.x86_64 lua-libs-5.4.7-3.fc43.x86_64 lua-srpm-macros-1-15.fc42.noarch lz4-libs-1.10.0-2.fc42.x86_64 mpfr-4.2.2-1.fc43.x86_64 ncurses-base-6.5-5.20250125.fc42.noarch ncurses-libs-6.5-5.20250125.fc42.x86_64 nettle-3.10.1-1.fc43.x86_64 npth-1.8-2.fc42.x86_64 ocaml-srpm-macros-10-4.fc42.noarch openblas-srpm-macros-2-19.fc42.noarch openldap-2.6.9-5.fc43.x86_64 openssl-libs-3.5.0-3.fc43.x86_64 p11-kit-0.25.5-8.fc43.x86_64 p11-kit-trust-0.25.5-8.fc43.x86_64 package-notes-srpm-macros-0.5-13.fc42.noarch pam-libs-1.7.0-4.fc42.x86_64 patch-2.8-1.fc43.x86_64 pcre2-10.45-1.fc43.x86_64 pcre2-syntax-10.45-1.fc43.noarch perl-srpm-macros-1-57.fc42.noarch pkgconf-2.3.0-2.fc42.x86_64 pkgconf-m4-2.3.0-2.fc42.noarch pkgconf-pkg-config-2.3.0-2.fc42.x86_64 popt-1.19-8.fc42.x86_64 publicsuffix-list-dafsa-20250116-1.fc42.noarch pyproject-srpm-macros-1.18.1-1.fc43.noarch python-srpm-macros-3.13-5.fc43.noarch qt5-srpm-macros-5.15.17-1.fc43.noarch qt6-srpm-macros-6.9.0-2.fc43.noarch readline-8.2-13.fc43.x86_64 redhat-rpm-config-343-6.fc43.noarch rpm-5.99.90-5.fc43.x86_64 rpm-build-5.99.90-5.fc43.x86_64 rpm-build-libs-5.99.90-5.fc43.x86_64 rpm-libs-5.99.90-5.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 rpm-sign-libs-5.99.90-5.fc43.x86_64 rust-srpm-macros-26.3-4.fc42.noarch sed-4.9-4.fc42.x86_64 setup-2.15.0-25.fc43.noarch shadow-utils-4.17.4-1.fc43.x86_64 sqlite-libs-3.50.0-1.fc43.x86_64 systemd-libs-257.6-1.fc43.x86_64 systemd-standalone-sysusers-257.6-1.fc43.x86_64 tar-1.35-5.fc42.x86_64 tpm2-tss-4.1.3-7.fc43.x86_64 tree-sitter-srpm-macros-0.2.4-1.fc43.noarch unzip-6.0-66.fc42.x86_64 util-linux-2.40.4-7.fc43.x86_64 util-linux-core-2.40.4-7.fc43.x86_64 which-2.23-1.fc42.x86_64 xxhash-libs-0.8.3-2.fc42.x86_64 xz-5.8.1-1.fc43.x86_64 xz-libs-5.8.1-1.fc43.x86_64 zig-srpm-macros-1-4.fc42.noarch zip-3.0-43.fc42.x86_64 zlib-ng-compat-2.2.4-2.fc43.x86_64 zstd-1.5.7-1.fc43.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1748908800 Wrote: /builddir/build/SRPMS/pymol-3.1.0-7.fc43.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1748989340.287934/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-vwtu97eg/pymol/pymol.spec) Config(child) 0 minutes 37 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-3.1.0-7.fc43.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1748989340.287934/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1748989340.287934/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-rawhide-x86_64-1748989340.287934/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-5.99.90-5.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 dnf5-5.2.13.1-2.fc43.x86_64 dnf5-plugins-5.2.13.1-2.fc43.x86_64 Finish: chroot init Start: build phase for pymol-3.1.0-7.fc43.src.rpm Start: build setup for pymol-3.1.0-7.fc43.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1748908800 Wrote: /builddir/build/SRPMS/pymol-3.1.0-7.fc43.src.rpm Updating and loading repositories: fedora 100% | 324.0 KiB/s | 10.0 KiB | 00m00s Copr repository 100% | 16.9 KiB/s | 1.5 KiB | 00m00s Coprdir repository 100% | 26.0 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: catch2-devel x86_64 2.13.10-6.fc42 fedora 952.9 KiB desktop-file-utils x86_64 0.28-1.fc43 fedora 218.4 KiB freeglut-devel x86_64 3.6.0-4.fc42 fedora 2.3 MiB freetype-devel x86_64 2.13.3-2.fc42 fedora 8.5 MiB gcc x86_64 15.1.1-2.fc43 fedora 111.1 MiB gcc-c++ x86_64 15.1.1-2.fc43 fedora 41.3 MiB glew-devel x86_64 2.2.0-10.fc42 fedora 1.8 MiB glm-devel noarch 1.0.1-4.fc43 fedora 2.1 MiB libappstream-glib x86_64 0.8.3-3.fc42 fedora 1.4 MiB libpng-devel x86_64 2:1.6.48-1.fc43 fedora 884.6 KiB libxml2-devel x86_64 2.12.10-1.fc43 fedora 3.4 MiB mesa-libGL-devel x86_64 25.1.1-1.fc43 fedora 80.8 KiB mmtf-cpp-devel x86_64 1.1.0-7.fc42 fedora 114.4 KiB msgpack-devel x86_64 3.1.0-18.fc42 fedora 5.1 MiB netcdf-devel x86_64 4.9.2-13.fc43 fedora 371.3 KiB pyproject-rpm-macros noarch 1.18.1-1.fc43 copr_base 114.5 KiB python3-devel x86_64 3.13.3-3.fc43 fedora 1.8 MiB python3-pillow x86_64 11.2.1-1.fc43 fedora 4.0 MiB python3-pyside6-devel x86_64 6.9.0-2.fc43 copr_base 2.9 MiB python3-pytest noarch 8.3.5-3.fc43 copr_base 3.7 MiB python3-qt5-devel x86_64 5.15.11-7.fc43 fedora 2.7 MiB Installing dependencies: OpenCL-ICD-Loader x86_64 3.0.6-2.20241023git5907ac1.fc42 fedora 70.7 KiB SDL3 x86_64 3.2.12-1.fc43 fedora 2.7 MiB abattis-cantarell-vf-fonts noarch 0.301-14.fc42 fedora 192.7 KiB abseil-cpp x86_64 20250512.0-1.fc43 fedora 2.3 MiB adwaita-cursor-theme noarch 48.0-2.fc43 fedora 11.4 MiB adwaita-icon-theme noarch 48.0-2.fc43 fedora 1.2 MiB adwaita-icon-theme-legacy noarch 46.2-3.fc42 fedora 2.1 MiB alsa-lib x86_64 1.2.14-2.fc43 fedora 1.4 MiB annobin-docs noarch 12.95-1.fc43 fedora 98.9 KiB annobin-plugin-gcc x86_64 12.95-1.fc43 fedora 993.6 KiB aribb24 x86_64 1.0.3^20160216git5e9be27-2.fc42 fedora 81.8 KiB assimp x86_64 5.4.3-1.fc43 fedora 7.4 MiB at-spi2-atk x86_64 2.56.2-1.fc43 fedora 275.6 KiB at-spi2-core x86_64 2.56.2-1.fc43 fedora 1.5 MiB atk x86_64 2.56.2-1.fc43 fedora 248.6 KiB authselect x86_64 1.5.1-1.fc43 fedora 153.9 KiB authselect-libs x86_64 1.5.1-1.fc43 fedora 825.0 KiB avahi x86_64 0.9~rc2-3.fc43 fedora 1.6 MiB avahi-devel x86_64 0.9~rc2-3.fc43 fedora 130.6 KiB avahi-glib x86_64 0.9~rc2-3.fc43 fedora 19.6 KiB avahi-libs x86_64 0.9~rc2-3.fc43 fedora 171.6 KiB blosc x86_64 1.21.6-6.fc42 fedora 126.2 KiB bluez-libs x86_64 5.83-1.fc43 fedora 198.3 KiB brotli x86_64 1.1.0-7.fc43 copr_base 31.6 KiB brotli-devel x86_64 1.1.0-7.fc43 copr_base 65.6 KiB bzip2-devel x86_64 1.0.8-20.fc42 fedora 309.8 KiB cairo x86_64 1.18.2-3.fc42 fedora 1.8 MiB cairo-devel x86_64 1.18.2-3.fc42 fedora 2.3 MiB cairo-gobject x86_64 1.18.2-3.fc42 fedora 35.1 KiB cdparanoia-libs x86_64 10.2-47.fc42 fedora 117.5 KiB cjson x86_64 1.7.18-2.fc42 fedora 63.9 KiB clang-libs x86_64 20.1.6-1.fc43 fedora 118.6 MiB clang-resource-filesystem x86_64 20.1.6-1.fc43 fedora 15.3 KiB cmake x86_64 3.31.6-2.fc43 fedora 34.2 MiB cmake-data noarch 3.31.6-2.fc43 fedora 8.5 MiB cmake-filesystem x86_64 3.31.6-2.fc43 fedora 0.0 B cmake-rpm-macros noarch 3.31.6-2.fc43 fedora 7.7 KiB codec2 x86_64 1.2.0-6.fc42 fedora 1.4 MiB colord-libs x86_64 1.4.7-6.fc42 fedora 850.7 KiB cpp x86_64 15.1.1-2.fc43 fedora 37.9 MiB cpuinfo x86_64 24.09.26-2.git1e83a2f.fc43.1 fedora 107.0 KiB cracklib x86_64 2.9.11-7.fc42 fedora 242.4 KiB cups-devel x86_64 1:2.4.12-3.fc43 fedora 185.8 KiB cups-filesystem noarch 1:2.4.12-3.fc43 fedora 0.0 B cups-libs x86_64 1:2.4.12-3.fc43 fedora 618.7 KiB dbus x86_64 1:1.16.0-3.fc42 fedora 0.0 B dbus-broker x86_64 36-7.fc43 fedora 383.1 KiB dbus-common noarch 1:1.16.0-3.fc42 fedora 11.2 KiB dbus-devel x86_64 1:1.16.0-3.fc42 fedora 131.7 KiB dbus-libs x86_64 1:1.16.0-3.fc42 fedora 349.5 KiB default-fonts-core-sans noarch 4.2-4.fc42 fedora 11.9 KiB double-conversion x86_64 3.3.1-3.fc43 fedora 97.6 KiB duktape x86_64 2.7.0-9.fc42 fedora 615.8 KiB emacs-filesystem noarch 1:30.0-4.fc42 fedora 0.0 B expat x86_64 2.7.1-1.fc43 fedora 294.2 KiB fdk-aac-free x86_64 2.0.0-15.fc42 fedora 615.8 KiB fftw-libs-single x86_64 3.3.10-15.fc42 fedora 3.6 MiB flac-libs x86_64 1.5.0-2.fc43 fedora 723.7 KiB fmt x86_64 11.2.0-2.fc43 fedora 266.9 KiB fontconfig x86_64 2.16.2-1.fc43 fedora 760.8 KiB fontconfig-devel x86_64 2.16.2-1.fc43 fedora 121.6 KiB fonts-filesystem noarch 1:2.0.5-22.fc43 fedora 0.0 B freeglut x86_64 3.6.0-4.fc42 fedora 475.7 KiB freetype x86_64 2.13.3-2.fc42 fedora 858.2 KiB fribidi x86_64 1.0.16-2.fc42 fedora 194.3 KiB game-music-emu x86_64 0.6.4-1.fc43 fedora 351.8 KiB gcc-gfortran x86_64 15.1.1-2.fc43 fedora 40.3 MiB gcc-plugin-annobin x86_64 15.1.1-2.fc43 fedora 57.2 KiB gdbm x86_64 1:1.23-9.fc42 fedora 460.3 KiB gdk-pixbuf2 x86_64 2.42.12-10.fc42 fedora 2.5 MiB gdk-pixbuf2-modules x86_64 2.42.12-10.fc42 fedora 63.4 KiB gettext x86_64 0.25-1.fc43 fedora 12.9 MiB gettext-envsubst x86_64 0.25-1.fc43 fedora 74.8 KiB gettext-libs x86_64 0.25-1.fc43 fedora 2.2 MiB gettext-runtime x86_64 0.25-1.fc43 fedora 444.2 KiB glib2 x86_64 2.85.0-1.fc43 fedora 14.7 MiB glib2-devel x86_64 2.85.0-1.fc43 fedora 15.9 MiB glibc-devel x86_64 2.41.9000-15.fc43 fedora 2.3 MiB glx-utils x86_64 9.0.0-9.fc42 fedora 418.6 KiB gmp-c++ x86_64 1:6.3.0-3.fc43 fedora 27.7 KiB gmp-devel x86_64 1:6.3.0-3.fc43 fedora 352.3 KiB gnutls-c++ x86_64 3.8.9-5.fc43 fedora 72.4 KiB gnutls-dane x86_64 3.8.9-5.fc43 fedora 69.3 KiB gnutls-devel x86_64 3.8.9-5.fc43 fedora 5.6 MiB google-noto-fonts-common noarch 20250501-1.fc43 fedora 17.7 KiB google-noto-sans-vf-fonts noarch 20250501-1.fc43 fedora 1.4 MiB graphene x86_64 1.10.6-10.fc42 fedora 162.4 KiB graphite2 x86_64 1.3.14-18.fc42 fedora 195.8 KiB graphite2-devel x86_64 1.3.14-18.fc42 fedora 49.3 KiB groff-base x86_64 1.23.0-8.fc42 fedora 3.9 MiB gsm x86_64 1.0.22-8.fc42 fedora 68.8 KiB gssdp x86_64 1.6.3-5.fc42 fedora 149.9 KiB gstreamer1 x86_64 1.26.2-1.fc43 fedora 5.3 MiB gstreamer1-plugins-bad-free-libs x86_64 1.26.2-1.fc43 fedora 3.1 MiB gstreamer1-plugins-base x86_64 1.26.2-1.fc43 fedora 7.3 MiB gtk-update-icon-cache x86_64 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fedora 5.9 MiB python3-qt5-base x86_64 5.15.11-7.fc43 fedora 15.5 MiB python3-rpm-generators noarch 14-12.fc42 fedora 81.7 KiB python3-rpm-macros noarch 3.13-5.fc43 fedora 6.4 KiB python3-shiboken6 x86_64 6.9.0-2.fc43 copr_base 627.9 KiB python3-shiboken6-devel x86_64 6.9.0-2.fc43 copr_base 3.3 MiB qt-settings noarch 42.0-4.fc43 fedora 1.1 KiB qt5-filesystem x86_64 5.15.17-1.fc43 fedora 0.0 B qt5-qtbase x86_64 5.15.17-1.fc43 fedora 10.0 MiB qt5-qtbase-common noarch 5.15.17-1.fc43 fedora 78.0 B qt5-qtbase-devel x86_64 5.15.17-1.fc43 fedora 19.1 MiB qt5-qtbase-gui x86_64 5.15.17-1.fc43 fedora 20.2 MiB qt5-qtconnectivity x86_64 5.15.17-1.fc43 fedora 1.4 MiB qt5-qtdeclarative x86_64 5.15.17-1.fc43 fedora 14.5 MiB qt5-qtlocation x86_64 5.15.17-1.fc43 fedora 10.8 MiB qt5-qtmultimedia x86_64 5.15.17-1.fc43 fedora 3.0 MiB qt5-qtsensors x86_64 5.15.17-1.fc43 fedora 922.9 KiB qt5-qtserialport x86_64 5.15.17-1.fc43 fedora 214.9 KiB qt5-qtsvg x86_64 5.15.17-1.fc43 fedora 627.3 KiB qt5-qttools-common noarch 5.15.17-1.fc43 fedora 7.5 KiB qt5-qttools-libs-designer x86_64 5.15.17-1.fc43 fedora 4.9 MiB qt5-qttools-libs-help x86_64 5.15.17-1.fc43 fedora 456.9 KiB qt5-qtwebchannel x86_64 5.15.17-1.fc43 fedora 307.1 KiB qt5-qtwebsockets x86_64 5.15.17-1.fc43 fedora 271.3 KiB qt5-qtx11extras x86_64 5.15.17-1.fc43 fedora 114.8 KiB qt5-qtxmlpatterns x86_64 5.15.17-1.fc43 fedora 2.9 MiB qt5-rpm-macros noarch 5.15.17-1.fc43 fedora 1.6 KiB qt6-assistant x86_64 6.9.0-1.fc43 fedora 1.6 MiB qt6-designer x86_64 6.9.0-1.fc43 fedora 606.7 KiB qt6-filesystem x86_64 6.9.0-2.fc43 fedora 0.0 B qt6-linguist x86_64 6.9.0-1.fc43 fedora 3.1 MiB qt6-qt3d x86_64 6.9.0-1.fc43 fedora 14.2 MiB qt6-qtbase x86_64 6.9.0-2.fc43 fedora 12.8 MiB qt6-qtbase-common noarch 6.9.0-2.fc43 fedora 74.0 B qt6-qtbase-devel x86_64 6.9.0-2.fc43 fedora 21.0 MiB qt6-qtbase-gui x86_64 6.9.0-2.fc43 fedora 23.6 MiB qt6-qtbase-ibase x86_64 6.9.0-2.fc43 fedora 153.6 KiB qt6-qtbase-mysql x86_64 6.9.0-2.fc43 fedora 113.5 KiB qt6-qtbase-odbc x86_64 6.9.0-2.fc43 fedora 141.1 KiB qt6-qtbase-postgresql x86_64 6.9.0-2.fc43 fedora 125.3 KiB qt6-qtbase-private-devel x86_64 6.9.0-2.fc43 fedora 4.5 MiB qt6-qtcharts x86_64 6.9.0-1.fc43 fedora 3.4 MiB qt6-qtconnectivity x86_64 6.9.0-1.fc43 fedora 1.5 MiB qt6-qtdatavis3d x86_64 6.9.0-1.fc43 fedora 2.3 MiB qt6-qtdeclarative x86_64 6.9.0-2.fc43 fedora 48.9 MiB qt6-qtdeclarative-devel x86_64 6.9.0-2.fc43 fedora 23.0 MiB qt6-qtgraphs x86_64 6.9.0-1.fc43 fedora 3.8 MiB qt6-qthttpserver x86_64 6.9.0-1.fc43 fedora 276.2 KiB qt6-qtimageformats x86_64 6.9.0-1.fc43 fedora 428.5 KiB qt6-qtlocation x86_64 6.9.0-1.fc43 fedora 2.7 MiB qt6-qtmultimedia x86_64 6.9.0-1.fc43 fedora 3.7 MiB qt6-qtnetworkauth x86_64 6.9.0-1.fc43 fedora 356.0 KiB qt6-qtpdf x86_64 6.9.0-2.fc43 fedora 23.2 MiB qt6-qtpositioning x86_64 6.9.0-1.fc43 fedora 1.5 MiB qt6-qtquick3d x86_64 6.9.0-1.fc43 fedora 12.5 MiB qt6-qtquicktimeline x86_64 6.9.0-1.fc43 fedora 283.3 KiB qt6-qtremoteobjects x86_64 6.9.0-1.fc43 fedora 1.4 MiB qt6-qtscxml x86_64 6.9.0-1.fc43 fedora 1.8 MiB qt6-qtsensors x86_64 6.9.0-1.fc43 fedora 925.2 KiB qt6-qtserialbus x86_64 6.9.0-1.fc43 fedora 900.0 KiB qt6-qtserialport x86_64 6.9.0-1.fc43 fedora 219.3 KiB qt6-qtshadertools x86_64 6.9.0-1.fc43 fedora 6.1 MiB qt6-qtspeech x86_64 6.9.0-1.fc43 fedora 361.5 KiB qt6-qtsvg x86_64 6.9.0-1.fc43 fedora 865.3 KiB qt6-qttools x86_64 6.9.0-1.fc43 fedora 840.6 KiB qt6-qttools-common noarch 6.9.0-1.fc43 fedora 7.5 KiB qt6-qttools-libs-designer x86_64 6.9.0-1.fc43 fedora 5.8 MiB qt6-qttools-libs-designercomponents x86_64 6.9.0-1.fc43 fedora 3.2 MiB qt6-qttools-libs-help x86_64 6.9.0-1.fc43 fedora 590.8 KiB qt6-qtwebchannel x86_64 6.9.0-1.fc43 fedora 415.6 KiB qt6-qtwebengine x86_64 6.9.0-2.fc43 fedora 253.6 MiB qt6-qtwebsockets x86_64 6.9.0-1.fc43 fedora 307.7 KiB qt6-qtwebview x86_64 6.9.0-1.fc43 fedora 335.1 KiB qt6-rpm-macros noarch 6.9.0-2.fc43 fedora 3.0 KiB rav1e-libs x86_64 0.7.1-5.fc42 fedora 3.0 MiB re2 x86_64 1:20240702-32.fc43 fedora 565.8 KiB rhash x86_64 1.4.5-2.fc42 fedora 351.0 KiB rsvg-pixbuf-loader x86_64 2.60.0-1.fc43 fedora 345.0 KiB samba-client-libs x86_64 2:4.22.1-1.fc43 copr_base 19.5 MiB samba-common noarch 2:4.22.1-1.fc43 copr_base 195.9 KiB samba-common-libs x86_64 2:4.22.1-1.fc43 copr_base 259.4 KiB sdl2-compat x86_64 2.32.56-1.fc43 fedora 399.6 KiB shared-mime-info x86_64 2.3-7.fc42 fedora 5.2 MiB shiboken6 x86_64 6.9.0-2.fc43 copr_base 104.3 KiB snappy x86_64 1.2.2-1.fc43 fedora 71.8 KiB soxr x86_64 0.1.3-18.fc42 fedora 191.5 KiB speex x86_64 1.2.0-19.fc42 fedora 128.5 KiB spirv-tools-libs x86_64 2025.2-1.fc43 fedora 5.8 MiB srt-libs x86_64 1.5.4-2.fc42 fedora 997.8 KiB svt-av1-libs x86_64 2.3.0-1.fc43 fedora 5.6 MiB sysprof-capture-devel x86_64 48.0-1.fc43 fedora 273.8 KiB systemd x86_64 257.6-1.fc43 fedora 12.1 MiB systemd-devel x86_64 257.6-1.fc43 fedora 600.4 KiB systemd-pam x86_64 257.6-1.fc43 fedora 1.1 MiB systemd-rpm-macros noarch 257.6-1.fc43 fedora 8.5 KiB systemd-shared x86_64 257.6-1.fc43 fedora 4.6 MiB tslib x86_64 1.23-1.fc43 fedora 416.1 KiB twolame-libs x86_64 0.4.0-6.fc42 fedora 165.5 KiB tzdata noarch 2025b-1.fc43 fedora 1.6 MiB unbound-libs x86_64 1.22.0-14.fc43 fedora 1.4 MiB unixODBC x86_64 2.3.12-6.fc42 fedora 1.0 MiB vim-filesystem noarch 2:9.1.1418-1.fc43 fedora 40.0 B vo-amrwbenc x86_64 0.1.3-22.fc42 fedora 153.9 KiB vulkan-headers noarch 1.4.313.0-1.fc43 fedora 30.9 MiB vulkan-loader x86_64 1.4.313.0-1.fc43 fedora 532.4 KiB vulkan-loader-devel x86_64 1.4.313.0-1.fc43 fedora 8.0 KiB webrtc-audio-processing x86_64 1.3-7.fc43 fedora 1.4 MiB xcb-util x86_64 0.4.1-7.fc42 fedora 26.3 KiB xcb-util-cursor x86_64 0.1.5-3.fc42 fedora 23.2 KiB xcb-util-image x86_64 0.4.1-7.fc42 fedora 22.2 KiB xcb-util-keysyms x86_64 0.4.1-7.fc42 fedora 16.7 KiB xcb-util-renderutil x86_64 0.3.10-7.fc42 fedora 24.4 KiB xcb-util-wm x86_64 0.4.2-7.fc42 fedora 81.2 KiB xkeyboard-config noarch 2.44-1.fc43 fedora 6.6 MiB xml-common noarch 0.6.3-66.fc42 fedora 78.4 KiB xorg-x11-proto-devel noarch 2024.1-4.fc42 fedora 1.7 MiB xprop x86_64 1.2.8-3.fc42 fedora 54.7 KiB xvidcore x86_64 1.3.7-13.fc42 fedora 878.4 KiB xz-devel x86_64 1:5.8.1-1.fc43 fedora 258.8 KiB zeromq x86_64 4.3.5-21.fc42 fedora 890.1 KiB zlib-ng-compat-devel x86_64 2.2.4-2.fc43 fedora 107.0 KiB zvbi x86_64 0.2.44-1.fc43 fedora 1.2 MiB Transaction Summary: Installing: 540 packages Total size of inbound packages is 545 MiB. Need to download 545 MiB. After this operation, 2 GiB extra will be used (install 2 GiB, remove 0 B). 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150.8 KiB | 00m00s [538/540] authselect-0:1.5.1-1.fc43.x86 100% | 1.7 MiB/s | 146.4 KiB | 00m00s [539/540] libpwquality-0:1.4.5-13.fc43. 100% | 6.6 MiB/s | 107.7 KiB | 00m00s [540/540] cracklib-0:2.9.11-7.fc42.x86_ 100% | 2.3 MiB/s | 91.6 KiB | 00m00s -------------------------------------------------------------------------------- [540/540] Total 100% | 35.2 MiB/s | 545.3 MiB | 00m16s Running transaction [ 1/542] Verify package files 100% | 512.0 B/s | 540.0 B | 00m01s [ 2/542] Prepare transaction 100% | 1.0 KiB/s | 540.0 B | 00m01s [ 3/542] Installing glib2-0:2.85.0-1.f 100% | 130.3 MiB/s | 14.7 MiB | 00m00s [ 4/542] Installing cmake-filesystem-0 100% | 1.9 MiB/s | 7.6 KiB | 00m00s [ 5/542] Installing dbus-libs-1:1.16.0 100% | 114.1 MiB/s | 350.6 KiB | 00m00s [ 6/542] Installing libpng-2:1.6.48-1. 100% | 116.7 MiB/s | 239.0 KiB | 00m00s [ 7/542] Installing libicu-0:76.1-4.fc 100% | 179.9 MiB/s | 36.3 MiB | 00m00s [ 8/542] Installing libjpeg-turbo-0:3. 100% | 157.2 MiB/s | 804.9 KiB | 00m00s [ 9/542] Installing expat-0:2.7.1-1.fc 100% | 16.1 MiB/s | 296.3 KiB | 00m00s [ 10/542] Installing zlib-ng-compat-dev 100% | 21.2 MiB/s | 108.5 KiB | 00m00s [ 11/542] Installing libX11-xcb-0:1.8.1 100% | 11.5 MiB/s | 11.8 KiB | 00m00s [ 12/542] Installing avahi-libs-0:0.9~r 100% | 85.0 MiB/s | 174.2 KiB | 00m00s [ 13/542] Installing libwayland-client- 100% | 61.8 MiB/s | 63.3 KiB | 00m00s [ 14/542] Installing nspr-0:4.36.0-9.fc 100% | 154.9 MiB/s | 317.2 KiB | 00m00s [ 15/542] Installing qt6-qttools-common 100% | 0.0 B/s | 7.9 KiB | 00m00s [ 16/542] Installing libogg-2:1.3.5-11. 100% | 11.4 MiB/s | 46.9 KiB | 00m00s [ 17/542] Installing nss-util-0:3.112.0 100% | 98.5 MiB/s | 201.8 KiB | 00m00s [ 18/542] Installing libtalloc-0:2.4.3- 100% | 63.7 MiB/s | 65.2 KiB | 00m00s [ 19/542] Installing opus-0:1.5.2-2.fc4 100% | 139.5 MiB/s | 428.6 KiB | 00m00s [ 20/542] Installing libglvnd-1:1.7.0-7 100% | 103.8 MiB/s | 531.6 KiB | 00m00s [ 21/542] Installing libglvnd-opengl-1: 100% | 73.0 MiB/s | 149.6 KiB | 00m00s [ 22/542] Installing libwebp-0:1.5.0-2. 100% | 154.9 MiB/s | 951.8 KiB | 00m00s [ 23/542] Installing lcms2-0:2.16-5.fc4 100% | 71.5 MiB/s | 439.3 KiB | 00m00s [ 24/542] Installing libvorbis-1:1.3.7- 100% | 204.1 MiB/s | 835.9 KiB | 00m00s [ 25/542] Installing libtirpc-0:1.3.6-1 100% | 98.0 MiB/s | 200.7 KiB | 00m00s [ 26/542] Installing alsa-lib-0:1.2.14- 100% | 49.8 MiB/s | 1.4 MiB | 00m00s [ 27/542] Installing pcre2-utf16-0:10.4 100% | 102.1 MiB/s | 627.2 KiB | 00m00s [ 28/542] Installing xorg-x11-proto-dev 100% | 99.0 MiB/s | 1.8 MiB | 00m00s [ 29/542] Installing libaec-0:1.1.3-2.f 100% | 49.0 MiB/s | 100.3 KiB | 00m00s [ 30/542] Installing openjpeg-0:2.5.3-6 100% | 73.9 MiB/s | 453.8 KiB | 00m00s [ 31/542] Installing libmpc-0:1.3.1-7.f 100% | 81.1 MiB/s | 166.1 KiB | 00m00s [ 32/542] Installing libtevent-0:0.16.2 100% | 50.1 MiB/s | 102.5 KiB | 00m00s [ 33/542] Installing libwayland-cursor- 100% | 37.5 MiB/s | 38.4 KiB | 00m00s [ 34/542] Installing json-glib-0:1.10.6 100% | 45.3 MiB/s | 602.5 KiB | 00m00s [ 35/542] Installing libsoup3-0:3.6.5-1 100% | 88.5 MiB/s | 1.2 MiB | 00m00s [ 36/542] Installing libtdb-0:1.4.13-2. 100% | 4.5 MiB/s | 101.6 KiB | 00m00s [ 37/542] Installing xml-common-0:0.6.3 100% | 26.4 MiB/s | 81.1 KiB | 00m00s [ 38/542] Installing fonts-filesystem-1 100% | 769.5 KiB/s | 788.0 B | 00m00s [ 39/542] Installing bluez-libs-0:5.83- 100% | 97.4 MiB/s | 199.4 KiB | 00m00s [ 40/542] Installing libICE-0:1.1.2-2.f 100% | 97.6 MiB/s | 199.8 KiB | 00m00s [ 41/542] Installing snappy-0:1.2.2-1.f 100% | 71.8 MiB/s | 73.5 KiB | 00m00s [ 42/542] Installing fribidi-0:1.0.16-2 100% | 2.9 MiB/s | 196.8 KiB | 00m00s [ 43/542] Installing python-rpm-macros- 100% | 22.3 MiB/s | 22.8 KiB | 00m00s [ 44/542] Installing python3-rpm-macros 100% | 6.5 MiB/s | 6.7 KiB | 00m00s [ 45/542] Installing libSM-0:1.2.5-2.fc 100% | 51.9 MiB/s | 106.4 KiB | 00m00s [ 46/542] Installing gssdp-0:1.6.3-5.fc 100% | 49.4 MiB/s | 151.9 KiB | 00m00s [ 47/542] Installing libtheora-1:1.1.1- 100% | 118.1 MiB/s | 483.7 KiB | 00m00s [ 48/542] Installing libpng-devel-2:1.6 100% | 29.9 MiB/s | 888.5 KiB | 00m00s [ 49/542] Installing shiboken6-0:6.9.0- 100% | 34.8 MiB/s | 106.8 KiB | 00m00s [ 50/542] Installing shared-mime-info-0 100% | 35.8 MiB/s | 2.6 MiB | 00m00s [ 51/542] Installing gdk-pixbuf2-0:2.42 100% | 54.9 MiB/s | 2.5 MiB | 00m00s [ 52/542] Installing libgudev-0:238-7.f 100% | 9.7 MiB/s | 89.3 KiB | 00m00s [ 53/542] Installing libseccomp-0:2.6.0 100% | 110.7 MiB/s | 226.8 KiB | 00m00s [ 54/542] Installing libtextstyle-0:0.2 100% | 97.8 MiB/s | 200.3 KiB | 00m00s [ 55/542] Installing gettext-libs-0:0.2 100% | 68.5 MiB/s | 2.2 MiB | 00m00s [ 56/542] Installing libquadmath-0:15.1 100% | 155.8 MiB/s | 319.2 KiB | 00m00s [ 57/542] Installing libidn2-devel-0:2. 100% | 17.0 MiB/s | 156.7 KiB | 00m00s [ 58/542] Installing kernel-headers-0:6 100% | 73.9 MiB/s | 6.7 MiB | 00m00s [ 59/542] Installing glibc-devel-0:2.41 100% | 31.2 MiB/s | 2.3 MiB | 00m00s [ 60/542] Installing libxcrypt-devel-0: 100% | 32.3 MiB/s | 33.1 KiB | 00m00s [ 61/542] Installing jsoncpp-0:1.9.6-1. 100% | 85.7 MiB/s | 263.1 KiB | 00m00s [ 62/542] Installing libdvdread-0:6.1.3 100% | 79.0 MiB/s | 161.8 KiB | 00m00s [ 63/542] Installing libvpl-1:2.14.0-2. 100% | 101.5 MiB/s | 415.6 KiB | 00m00s [ 64/542] Installing liblc3-0:1.1.3-1.f 100% | 11.2 MiB/s | 171.8 KiB | 00m00s [ 65/542] Installing libdav1d-0:1.5.1-1 100% | 60.5 MiB/s | 1.7 MiB | 00m00s [ 66/542] Installing fdk-aac-free-0:2.0 100% | 120.6 MiB/s | 617.3 KiB | 00m00s [ 67/542] Installing noopenh264-0:2.6.0 100% | 19.9 MiB/s | 40.7 KiB | 00m00s [ 68/542] Installing libxslt-0:1.1.43-1 100% | 13.6 MiB/s | 459.2 KiB | 00m00s [ 69/542] Installing mpg123-libs-0:1.32 100% | 132.9 MiB/s | 816.6 KiB | 00m00s [ 70/542] Installing lame-libs-0:3.100- 100% | 120.3 MiB/s | 1.2 MiB | 00m00s [ 71/542] Installing gsm-0:1.0.22-8.fc4 100% | 34.4 MiB/s | 70.4 KiB | 00m00s [ 72/542] Installing pixman-0:0.44.2-2. 100% | 164.9 MiB/s | 675.3 KiB | 00m00s [ 73/542] Installing spirv-tools-libs-0 100% | 107.1 MiB/s | 5.8 MiB | 00m00s [ 74/542] Installing mesa-filesystem-0: 100% | 4.2 MiB/s | 4.3 KiB | 00m00s [ 75/542] Installing libwayland-egl-0:1 100% | 1.7 MiB/s | 13.6 KiB | 00m00s [ 76/542] Installing vulkan-loader-0:1. 100% | 104.5 MiB/s | 535.0 KiB | 00m00s [ 77/542] Installing libunwind-0:1.8.1- 100% | 64.3 MiB/s | 197.4 KiB | 00m00s [ 78/542] Installing mtdev-0:1.1.6-10.f 100% | 29.7 MiB/s | 30.4 KiB | 00m00s [ 79/542] Installing libevdev-0:1.13.4- 100% | 40.6 MiB/s | 83.1 KiB | 00m00s [ 80/542] Installing libwayland-server- 100% | 5.2 MiB/s | 79.8 KiB | 00m00s [ 81/542] Installing qt5-qttools-common 100% | 7.7 MiB/s | 7.9 KiB | 00m00s [ 82/542] Installing double-conversion- 100% | 48.5 MiB/s | 99.4 KiB | 00m00s [ 83/542] Installing libgfortran-0:15.1 100% | 88.0 MiB/s | 3.3 MiB | 00m00s [ 84/542] Installing hdf5-0:1.14.6-3.fc 100% | 81.2 MiB/s | 6.4 MiB | 00m00s [ 85/542] Installing graphite2-0:1.3.14 100% | 11.4 MiB/s | 197.9 KiB | 00m00s [ 86/542] Installing harfbuzz-0:11.2.1- 100% | 68.2 MiB/s | 2.8 MiB | 00m00s [ 87/542] Installing freetype-0:2.13.3- 100% | 140.0 MiB/s | 859.9 KiB | 00m00s [ 88/542] Installing libXau-0:1.0.12-2. 100% | 4.8 MiB/s | 78.5 KiB | 00m00s [ 89/542] Installing libxcb-0:1.17.0-5. 100% | 90.0 MiB/s | 1.1 MiB | 00m00s [ 90/542] Installing xcb-util-renderuti 100% | 25.2 MiB/s | 25.8 KiB | 00m00s [ 91/542] Installing xcb-util-keysyms-0 100% | 17.4 MiB/s | 17.8 KiB | 00m00s [ 92/542] Installing xcb-util-wm-0:0.4. 100% | 1.0 MiB/s | 83.2 KiB | 00m00s [ 93/542] Installing libb2-0:0.98.1-13. 100% | 46.1 MiB/s | 47.2 KiB | 00m00s [ 94/542] Installing make-1:4.4.1-10.fc 100% | 40.0 MiB/s | 1.8 MiB | 00m00s [ 95/542] Installing emacs-filesystem-1 100% | 531.2 KiB/s | 544.0 B | 00m00s [ 96/542] Installing xcb-util-0:0.4.1-7 100% | 27.0 MiB/s | 27.7 KiB | 00m00s [ 97/542] Installing xcb-util-image-0:0 100% | 23.0 MiB/s | 23.6 KiB | 00m00s [ 98/542] Installing xcb-util-cursor-0: 100% | 24.0 MiB/s | 24.6 KiB | 00m00s [ 99/542] Installing libXau-devel-0:1.0 100% | 1.3 MiB/s | 9.4 KiB | 00m00s [100/542] Installing libxcb-devel-0:1.1 100% | 16.4 MiB/s | 3.1 MiB | 00m00s [101/542] Installing libraqm-0:0.10.1-2 100% | 14.5 MiB/s | 29.7 KiB | 00m00s [102/542] Installing harfbuzz-icu-0:11. 100% | 15.9 MiB/s | 16.3 KiB | 00m00s [103/542] Installing graphite2-devel-0: 100% | 49.6 MiB/s | 50.8 KiB | 00m00s [104/542] Installing pixman-devel-0:0.4 100% | 2.5 MiB/s | 50.2 KiB | 00m00s [105/542] Installing libopenmpt-0:0.7.1 100% | 165.3 MiB/s | 1.7 MiB | 00m00s [106/542] Installing libdvdnav-0:6.1.1- 100% | 13.2 MiB/s | 121.7 KiB | 00m00s [107/542] Installing openxr-libs-0:1.1. 100% | 87.7 MiB/s | 269.3 KiB | 00m00s [108/542] Installing systemd-shared-0:2 100% | 121.9 MiB/s | 4.6 MiB | 00m00s [109/542] Installing gtk-update-icon-ca 100% | 3.9 MiB/s | 63.3 KiB | 00m00s [110/542] Installing pyproject-rpm-macr 100% | 5.7 MiB/s | 116.4 KiB | 00m00s [111/542] Installing blosc-0:1.21.6-6.f 100% | 42.0 MiB/s | 129.0 KiB | 00m00s [112/542] Installing abattis-cantarell- 100% | 47.5 MiB/s | 194.4 KiB | 00m00s [113/542] Installing iso-codes-0:4.18.0 100% | 86.9 MiB/s | 21.6 MiB | 00m00s [114/542] Installing libgusb-0:0.4.9-3. 100% | 53.3 MiB/s | 163.7 KiB | 00m00s [115/542] Installing colord-libs-0:1.4. 100% | 166.7 MiB/s | 853.7 KiB | 00m00s [116/542] Installing cpp-0:15.1.1-2.fc4 100% | 79.7 MiB/s | 37.9 MiB | 00m00s [117/542] Installing gcc-0:15.1.1-2.fc4 100% | 122.5 MiB/s | 111.2 MiB | 00m01s [118/542] Installing libquadmath-devel- 100% | 11.5 MiB/s | 23.6 KiB | 00m00s [119/542] Installing gcc-gfortran-0:15. 100% | 152.7 MiB/s | 40.3 MiB | 00m00s [120/542] Installing libaec-devel-0:1.1 100% | 6.6 MiB/s | 13.5 KiB | 00m00s [121/542] Installing hdf5-devel-0:1.14. 100% | 101.2 MiB/s | 3.3 MiB | 00m00s [122/542] Installing hdf-libs-0:4.3.0-3 100% | 96.0 MiB/s | 688.3 KiB | 00m00s [123/542] Installing libnsl2-0:2.0.1-3. 100% | 57.6 MiB/s | 59.0 KiB | 00m00s [124/542] Installing libmng-0:2.0.3-23. 100% | 177.2 MiB/s | 544.3 KiB | 00m00s [125/542] Installing mesa-libGLU-0:9.0. 100% | 70.8 MiB/s | 362.6 KiB | 00m00s [126/542] Installing nss-softokn-freebl 100% | 166.1 MiB/s | 850.5 KiB | 00m00s [127/542] Installing nss-softokn-0:3.11 100% | 171.8 MiB/s | 1.9 MiB | 00m00s [128/542] Installing nss-0:3.112.0-1.fc 100% | 64.8 MiB/s | 1.9 MiB | 00m00s [129/542] Installing nss-sysinit-0:3.11 100% | 959.4 KiB/s | 19.2 KiB | 00m00s [130/542] Installing flac-libs-0:1.5.0- 100% | 141.9 MiB/s | 726.4 KiB | 00m00s [131/542] Installing libsndfile-0:1.2.2 100% | 67.3 MiB/s | 551.6 KiB | 00m00s [132/542] Installing avahi-glib-0:0.9~r 100% | 19.8 MiB/s | 20.3 KiB | 00m00s [133/542] Installing libtinysparql-0:3. 100% | 129.7 MiB/s | 1.3 MiB | 00m00s [134/542] Installing jasper-libs-0:4.2. 100% | 84.8 MiB/s | 347.3 KiB | 00m00s [135/542] Installing libicu-devel-0:76. 100% | 61.1 MiB/s | 5.1 MiB | 00m00s [136/542] Installing aribb24-0:1.0.3^20 100% | 40.6 MiB/s | 83.2 KiB | 00m00s [137/542] Installing zvbi-0:0.2.44-1.fc 100% | 10.8 MiB/s | 1.2 MiB | 00m00s [138/542] Installing libssh-devel-0:0.1 100% | 58.8 MiB/s | 180.5 KiB | 00m00s [139/542] Installing graphene-0:1.10.6- 100% | 80.1 MiB/s | 164.1 KiB | 00m00s [140/542] Installing libcloudproviders- 100% | 41.1 MiB/s | 126.2 KiB | 00m00s [141/542] Installing cracklib-0:2.9.11- 100% | 6.4 MiB/s | 253.7 KiB | 00m00s [142/542] Installing libpwquality-0:1.4 100% | 13.3 MiB/s | 421.6 KiB | 00m00s [143/542] Installing gdbm-1:1.23-9.fc42 100% | 6.1 MiB/s | 465.2 KiB | 00m00s [144/542] Installing authselect-libs-0: 100% | 63.1 MiB/s | 840.0 KiB | 00m00s [145/542] Installing annobin-docs-0:12. 100% | 14.0 MiB/s | 100.0 KiB | 00m00s [146/542] Installing OpenCL-ICD-Loader- 100% | 3.2 MiB/s | 71.8 KiB | 00m00s >>> Running sysusers scriptlet: dbus-common-1:1.16.0-3.fc42.noarch >>> Finished sysusers scriptlet: dbus-common-1:1.16.0-3.fc42.noarch >>> Scriptlet output: >>> Creating group 'dbus' with GID 81. >>> Creating user 'dbus' (System Message Bus) with UID 81 and GID 81. >>> [147/542] Installing dbus-common-1:1.16 100% | 387.2 KiB/s | 13.6 KiB | 00m00s [148/542] Installing dbus-broker-0:36-7 100% | 8.4 MiB/s | 385.7 KiB | 00m00s [149/542] Installing dbus-1:1.16.0-3.fc 100% | 2.9 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: systemd-0:257.6-1.fc43.x86_64 >>> Finished sysusers scriptlet: systemd-0:257.6-1.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'systemd-journal' with GID 190. >>> >>> Running sysusers scriptlet: systemd-0:257.6-1.fc43.x86_64 >>> Finished sysusers scriptlet: systemd-0:257.6-1.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'systemd-oom' with GID 999. >>> Creating user 'systemd-oom' (systemd Userspace OOM Killer) with UID 999 and >>> [150/542] Installing systemd-0:257.6-1. 100% | 31.9 MiB/s | 12.2 MiB | 00m00s [151/542] Installing systemd-pam-0:257. 100% | 20.4 MiB/s | 1.1 MiB | 00m00s >>> Running sysusers scriptlet: samba-common-2:4.22.1-1.fc43.noarch >>> Finished sysusers scriptlet: samba-common-2:4.22.1-1.fc43.noarch >>> Scriptlet output: >>> Creating group 'printadmin' with GID 998. >>> [152/542] Installing samba-common-2:4.2 100% | 7.5 MiB/s | 199.4 KiB | 00m00s [153/542] Installing gupnp-0:1.6.8-1.fc 100% | 75.6 MiB/s | 309.8 KiB | 00m00s [154/542] Installing gupnp-igd-0:1.6.0- 100% | 35.4 MiB/s | 72.5 KiB | 00m00s [155/542] Installing libnice-0:0.1.22-7 100% | 23.3 MiB/s | 500.6 KiB | 00m00s [156/542] Installing libblkid-devel-0:2 100% | 22.5 MiB/s | 46.0 KiB | 00m00s [157/542] Installing gettext-envsubst-0 100% | 3.9 MiB/s | 76.2 KiB | 00m00s [158/542] Installing gettext-runtime-0: 100% | 14.8 MiB/s | 453.6 KiB | 00m00s [159/542] Installing gettext-0:0.25-1.f 100% | 143.8 MiB/s | 12.9 MiB | 00m00s [160/542] Installing systemd-devel-0:25 100% | 11.9 MiB/s | 729.5 KiB | 00m00s [161/542] Installing dbus-devel-1:1.16. 100% | 33.3 MiB/s | 136.5 KiB | 00m00s [162/542] Installing sysprof-capture-de 100% | 90.1 MiB/s | 276.7 KiB | 00m00s [163/542] Installing libffi-devel-0:3.4 100% | 17.0 MiB/s | 34.8 KiB | 00m00s [164/542] Installing p11-kit-devel-0:0. 100% | 54.9 MiB/s | 562.7 KiB | 00m00s [165/542] Installing gmp-c++-1:6.3.0-3. 100% | 27.8 MiB/s | 28.5 KiB | 00m00s [166/542] Installing gmp-devel-1:6.3.0- 100% | 172.9 MiB/s | 354.1 KiB | 00m00s [167/542] Installing nettle-devel-0:3.1 100% | 102.8 MiB/s | 1.5 MiB | 00m00s [168/542] Installing libtasn1-tools-0:4 100% | 2.7 MiB/s | 63.1 KiB | 00m00s [169/542] Installing libtasn1-devel-0:4 100% | 20.3 MiB/s | 83.1 KiB | 00m00s [170/542] Installing pcre2-utf32-0:10.4 100% | 117.0 MiB/s | 599.1 KiB | 00m00s [171/542] Installing pcre2-devel-0:10.4 100% | 46.5 MiB/s | 2.1 MiB | 00m00s [172/542] Installing lmdb-libs-0:0.9.33 100% | 34.8 MiB/s | 106.9 KiB | 00m00s [173/542] Installing samba-common-libs- 100% | 28.4 MiB/s | 261.4 KiB | 00m00s [174/542] Installing samba-client-libs- 100% | 100.7 MiB/s | 19.5 MiB | 00m00s [175/542] Installing libldb-2:4.22.1-1. 100% | 18.6 MiB/s | 456.1 KiB | 00m00s [176/542] Installing libwbclient-2:4.22 100% | 33.9 MiB/s | 69.3 KiB | 00m00s [177/542] Installing libsmbclient-2:4.2 100% | 80.8 MiB/s | 165.4 KiB | 00m00s [178/542] Installing protobuf-c-0:1.5.1 100% | 50.2 MiB/s | 51.4 KiB | 00m00s [179/542] Installing hiredis-0:1.2.0-6. 100% | 105.1 MiB/s | 107.6 KiB | 00m00s [180/542] Installing gnutls-c++-0:3.8.9 100% | 71.5 MiB/s | 73.2 KiB | 00m00s [181/542] Installing libdaemon-0:0.14-3 100% | 4.0 MiB/s | 69.6 KiB | 00m00s >>> Running sysusers scriptlet: avahi-0:0.9~rc2-3.fc43.x86_64 >>> Finished sysusers scriptlet: avahi-0:0.9~rc2-3.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'avahi' with GID 70. >>> Creating user 'avahi' (Avahi mDNS/DNS-SD Stack) with UID 70 and GID 70. >>> [182/542] Installing avahi-0:0.9~rc2-3. 100% | 25.5 MiB/s | 1.6 MiB | 00m00s >>> Running post-install scriptlet: avahi-0:0.9~rc2-3.fc43.x86_64 >>> Finished post-install scriptlet: avahi-0:0.9~rc2-3.fc43.x86_64 >>> 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 >>> [183/542] Installing bzip2-devel-0:1.0. 100% | 60.7 MiB/s | 310.7 KiB | 00m00s [184/542] Installing libstdc++-devel-0: 100% | 55.9 MiB/s | 16.2 MiB | 00m00s [185/542] Installing gcc-c++-0:15.1.1-2 100% | 77.8 MiB/s | 41.3 MiB | 00m01s [186/542] Installing libverto-devel-0:0 100% | 25.7 MiB/s | 26.4 KiB | 00m00s [187/542] Installing libsepol-devel-0:3 100% | 25.1 MiB/s | 128.3 KiB | 00m00s [188/542] Installing libselinux-devel-0 100% | 12.1 MiB/s | 161.6 KiB | 00m00s [189/542] Installing libmount-devel-0:2 100% | 63.0 MiB/s | 64.5 KiB | 00m00s [190/542] Installing libcom_err-devel-0 100% | 961.8 KiB/s | 18.3 KiB | 00m00s [191/542] Installing keyutils-libs-deve 100% | 3.4 MiB/s | 55.2 KiB | 00m00s [192/542] Installing openssl-devel-1:3. 100% | 17.8 MiB/s | 5.6 MiB | 00m00s [193/542] Installing publicsuffix-list- 100% | 161.5 MiB/s | 330.8 KiB | 00m00s [194/542] Installing libpsl-devel-0:0.2 100% | 55.5 MiB/s | 113.6 KiB | 00m00s [195/542] Installing libnghttp2-devel-0 100% | 70.2 MiB/s | 287.5 KiB | 00m00s [196/542] Installing libkadm5-0:1.21.3- 100% | 105.4 MiB/s | 215.9 KiB | 00m00s [197/542] Installing krb5-devel-0:1.21. 100% | 34.9 MiB/s | 715.2 KiB | 00m00s [198/542] Installing brotli-0:1.1.0-7.f 100% | 2.1 MiB/s | 32.3 KiB | 00m00s [199/542] Installing brotli-devel-0:1.1 100% | 22.1 MiB/s | 68.0 KiB | 00m00s [200/542] Installing libcurl-devel-0:8. 100% | 26.2 MiB/s | 1.4 MiB | 00m00s [201/542] Installing python-pip-wheel-0 100% | 415.0 MiB/s | 1.2 MiB | 00m00s [202/542] Installing ncurses-0:6.5-5.20 100% | 12.3 MiB/s | 614.7 KiB | 00m00s [203/542] Installing groff-base-0:1.23. 100% | 59.0 MiB/s | 3.9 MiB | 00m00s [204/542] Installing perl-Digest-0:1.20 100% | 18.1 MiB/s | 37.1 KiB | 00m00s [205/542] Installing perl-Digest-MD5-0: 100% | 30.1 MiB/s | 61.6 KiB | 00m00s [206/542] Installing perl-FileHandle-0: 100% | 9.5 MiB/s | 9.8 KiB | 00m00s [207/542] Installing perl-B-0:1.89-517. 100% | 163.2 MiB/s | 501.3 KiB | 00m00s [208/542] Installing perl-libnet-0:3.15 100% | 71.9 MiB/s | 294.7 KiB | 00m00s [209/542] Installing perl-Data-Dumper-0 100% | 57.4 MiB/s | 117.5 KiB | 00m00s [210/542] Installing perl-MIME-Base32-0 100% | 31.4 MiB/s | 32.2 KiB | 00m00s [211/542] Installing perl-URI-0:5.32-1. 100% | 24.3 MiB/s | 274.1 KiB | 00m00s [212/542] Installing perl-AutoLoader-0: 100% | 20.5 MiB/s | 20.9 KiB | 00m00s [213/542] Installing perl-IO-Socket-IP- 100% | 99.8 MiB/s | 102.2 KiB | 00m00s [214/542] Installing perl-IO-Socket-SSL 100% | 172.7 MiB/s | 707.4 KiB | 00m00s [215/542] Installing perl-Net-SSLeay-0: 100% | 97.0 MiB/s | 1.4 MiB | 00m00s [216/542] Installing perl-locale-0:1.12 100% | 6.7 MiB/s | 6.9 KiB | 00m00s [217/542] Installing perl-if-0:0.61.000 100% | 0.0 B/s | 6.2 KiB | 00m00s [218/542] Installing perl-Text-Tabs+Wra 100% | 23.3 MiB/s | 23.9 KiB | 00m00s [219/542] Installing perl-Pod-Escapes-1 100% | 25.3 MiB/s | 25.9 KiB | 00m00s [220/542] Installing perl-Time-Local-2: 100% | 68.9 MiB/s | 70.6 KiB | 00m00s [221/542] Installing perl-File-Path-0:2 100% | 63.0 MiB/s | 64.5 KiB | 00m00s [222/542] Installing perl-HTTP-Tiny-0:0 100% | 76.4 MiB/s | 156.4 KiB | 00m00s [223/542] Installing perl-Pod-Simple-1: 100% | 112.3 MiB/s | 574.8 KiB | 00m00s [224/542] Installing perl-POSIX-0:2.20- 100% | 37.8 MiB/s | 232.3 KiB | 00m00s [225/542] Installing perl-IPC-Open3-0:1 100% | 22.7 MiB/s | 23.3 KiB | 00m00s [226/542] Installing perl-File-Temp-1:0 100% | 80.1 MiB/s | 164.1 KiB | 00m00s [227/542] Installing perl-Term-Cap-0:1. 100% | 29.9 MiB/s | 30.6 KiB | 00m00s [228/542] Installing perl-Term-ANSIColo 100% | 96.9 MiB/s | 99.2 KiB | 00m00s [229/542] Installing perl-Class-Struct- 100% | 25.3 MiB/s | 25.9 KiB | 00m00s [230/542] Installing perl-Pod-Perldoc-0 100% | 8.7 MiB/s | 169.2 KiB | 00m00s [231/542] Installing perl-podlators-1:6 100% | 17.4 MiB/s | 321.4 KiB | 00m00s [232/542] Installing perl-File-stat-0:1 100% | 2.1 MiB/s | 13.1 KiB | 00m00s [233/542] Installing perl-Symbol-0:1.09 100% | 0.0 B/s | 7.2 KiB | 00m00s [234/542] Installing perl-SelectSaver-0 100% | 0.0 B/s | 2.6 KiB | 00m00s [235/542] Installing perl-Socket-4:2.03 100% | 59.6 MiB/s | 122.0 KiB | 00m00s [236/542] Installing perl-Pod-Usage-4:2 100% | 5.0 MiB/s | 87.9 KiB | 00m00s [237/542] Installing perl-IO-0:1.55-517 100% | 49.2 MiB/s | 151.3 KiB | 00m00s [238/542] Installing perl-overloading-0 100% | 5.4 MiB/s | 5.5 KiB | 00m00s [239/542] Installing perl-mro-0:1.29-51 100% | 41.6 MiB/s | 42.6 KiB | 00m00s [240/542] Installing perl-Fcntl-0:1.18- 100% | 48.8 MiB/s | 50.0 KiB | 00m00s [241/542] Installing perl-base-0:2.27-5 100% | 0.0 B/s | 12.9 KiB | 00m00s [242/542] Installing perl-Text-ParseWor 100% | 14.2 MiB/s | 14.6 KiB | 00m00s [243/542] Installing perl-File-Basename 100% | 14.2 MiB/s | 14.6 KiB | 00m00s [244/542] Installing perl-Getopt-Long-1 100% | 71.9 MiB/s | 147.2 KiB | 00m00s [245/542] Installing perl-Storable-1:3. 100% | 2.7 MiB/s | 233.9 KiB | 00m00s [246/542] Installing perl-Getopt-Std-0: 100% | 11.5 MiB/s | 11.7 KiB | 00m00s [247/542] Installing perl-MIME-Base64-0 100% | 21.6 MiB/s | 44.3 KiB | 00m00s [248/542] Installing perl-parent-1:0.24 100% | 10.7 MiB/s | 11.0 KiB | 00m00s [249/542] Installing perl-overload-0:1. 100% | 70.3 MiB/s | 71.9 KiB | 00m00s [250/542] Installing perl-Scalar-List-U 100% | 48.3 MiB/s | 148.5 KiB | 00m00s [251/542] Installing perl-Errno-0:1.38- 100% | 0.0 B/s | 8.7 KiB | 00m00s [252/542] Installing perl-constant-0:1. 100% | 26.7 MiB/s | 27.4 KiB | 00m00s [253/542] Installing perl-vars-0:1.05-5 100% | 4.2 MiB/s | 4.3 KiB | 00m00s [254/542] Installing perl-Encode-4:3.21 100% | 54.0 MiB/s | 4.7 MiB | 00m00s [255/542] Installing perl-DynaLoader-0: 100% | 31.7 MiB/s | 32.5 KiB | 00m00s [256/542] Installing perl-PathTools-0:3 100% | 60.1 MiB/s | 184.5 KiB | 00m00s [257/542] Installing perl-Exporter-0:5. 100% | 54.3 MiB/s | 55.6 KiB | 00m00s [258/542] Installing perl-Carp-0:1.54-5 100% | 15.5 MiB/s | 47.7 KiB | 00m00s [259/542] Installing perl-libs-4:5.40.2 100% | 74.4 MiB/s | 9.9 MiB | 00m00s [260/542] Installing perl-interpreter-4 100% | 6.9 MiB/s | 119.9 KiB | 00m00s [261/542] Installing perl-English-0:1.1 100% | 6.5 MiB/s | 6.6 KiB | 00m00s [262/542] Installing perl-File-Find-0:1 100% | 41.5 MiB/s | 42.5 KiB | 00m00s [263/542] Installing vim-filesystem-2:9 100% | 2.3 MiB/s | 4.7 KiB | 00m00s [264/542] Installing rhash-0:1.4.5-2.fc 100% | 18.3 MiB/s | 356.4 KiB | 00m00s [265/542] Installing libuv-1:1.51.0-1.f 100% | 46.6 MiB/s | 573.0 KiB | 00m00s [266/542] Installing mariadb-connector- 100% | 0.0 B/s | 1.0 KiB | 00m00s [267/542] Installing mariadb-connector- 100% | 101.2 MiB/s | 517.9 KiB | 00m00s [268/542] Installing libtommath-0:1.3.1 100% | 128.4 MiB/s | 131.5 KiB | 00m00s [269/542] Installing libfbclient2-0:4.0 100% | 171.5 MiB/s | 3.1 MiB | 00m00s [270/542] Installing libpq-0:16.4-2.fc4 100% | 43.0 MiB/s | 969.5 KiB | 00m00s [271/542] Installing unixODBC-0:2.3.12- 100% | 35.0 MiB/s | 1.0 MiB | 00m00s [272/542] Installing openpgm-0:5.3.128- 100% | 103.4 MiB/s | 317.7 KiB | 00m00s [273/542] Installing libsodium-0:1.0.20 100% | 127.0 MiB/s | 390.2 KiB | 00m00s [274/542] Installing zeromq-0:4.3.5-21. 100% | 36.7 MiB/s | 902.7 KiB | 00m00s [275/542] Installing mbedtls-0:3.6.3-1. 100% | 93.5 MiB/s | 1.3 MiB | 00m00s [276/542] Installing cjson-0:1.7.18-2.f 100% | 1.8 MiB/s | 65.3 KiB | 00m00s [277/542] Installing librist-0:0.2.7-9. 100% | 51.7 MiB/s | 158.8 KiB | 00m00s [278/542] Installing libudfread-0:1.1.2 100% | 65.8 MiB/s | 67.3 KiB | 00m00s [279/542] Installing cpuinfo-0:24.09.26 100% | 5.6 MiB/s | 109.7 KiB | 00m00s [280/542] Installing svt-av1-libs-0:2.3 100% | 125.0 MiB/s | 5.6 MiB | 00m00s [281/542] Installing highway-0:1.2.0-5. 100% | 145.1 MiB/s | 4.4 MiB | 00m00s [282/542] Installing libjxl-1:0.11.1-2. 100% | 84.6 MiB/s | 3.0 MiB | 00m00s [283/542] Installing libvmaf-0:3.0.0-3. 100% | 202.2 MiB/s | 828.4 KiB | 00m00s [284/542] Installing libaom-0:3.12.0-1. 100% | 76.8 MiB/s | 5.0 MiB | 00m00s [285/542] Installing lpcnetfreedv-0:0.5 100% | 72.7 MiB/s | 14.8 MiB | 00m00s [286/542] Installing codec2-0:1.2.0-6.f 100% | 24.9 MiB/s | 1.4 MiB | 00m00s [287/542] Installing abseil-cpp-0:20250 100% | 97.6 MiB/s | 2.3 MiB | 00m00s [288/542] Installing re2-1:20240702-32. 100% | 138.5 MiB/s | 567.2 KiB | 00m00s [289/542] Installing webrtc-audio-proce 100% | 85.4 MiB/s | 1.4 MiB | 00m00s [290/542] Installing libsbc-0:2.0-6.fc4 100% | 92.3 MiB/s | 94.5 KiB | 00m00s [291/542] Installing libldac-0:2.0.2.3- 100% | 82.2 MiB/s | 84.2 KiB | 00m00s [292/542] Installing libebur128-0:1.2.6 100% | 39.8 MiB/s | 40.7 KiB | 00m00s [293/542] Installing fftw-libs-single-0 100% | 181.0 MiB/s | 3.6 MiB | 00m00s [294/542] Installing pugixml-0:1.14-2.f 100% | 130.9 MiB/s | 268.1 KiB | 00m00s [295/542] Installing poly2tri-0:0.0^201 100% | 56.1 MiB/s | 57.5 KiB | 00m00s [296/542] Installing assimp-0:5.4.3-1.f 100% | 102.3 MiB/s | 7.4 MiB | 00m00s [297/542] Installing soxr-0:0.1.3-18.fc 100% | 63.0 MiB/s | 193.6 KiB | 00m00s [298/542] Installing srt-libs-0:1.5.4-2 100% | 243.9 MiB/s | 998.9 KiB | 00m00s [299/542] Installing librabbitmq-0:0.15 100% | 3.5 MiB/s | 90.7 KiB | 00m00s [300/542] Installing libmodplug-1:0.8.9 100% | 116.2 MiB/s | 357.0 KiB | 00m00s [301/542] Installing game-music-emu-0:0 100% | 172.5 MiB/s | 353.2 KiB | 00m00s [302/542] Installing xvidcore-0:1.3.7-1 100% | 122.8 MiB/s | 880.1 KiB | 00m00s [303/542] Installing vo-amrwbenc-0:0.1. 100% | 75.9 MiB/s | 155.4 KiB | 00m00s [304/542] Installing twolame-libs-0:0.4 100% | 162.7 MiB/s | 166.6 KiB | 00m00s [305/542] Installing speex-0:1.2.0-19.f 100% | 63.7 MiB/s | 130.4 KiB | 00m00s [306/542] Installing rav1e-libs-0:0.7.1 100% | 201.2 MiB/s | 3.0 MiB | 00m00s [307/542] Installing opencore-amr-0:0.1 100% | 114.3 MiB/s | 351.2 KiB | 00m00s [308/542] Installing libvpx-0:1.15.0-2. 100% | 191.5 MiB/s | 3.3 MiB | 00m00s [309/542] Installing ilbc-0:3.0.4-15.fc 100% | 45.4 MiB/s | 92.9 KiB | 00m00s [310/542] Installing minizip-ng-compat- 100% | 17.7 MiB/s | 163.3 KiB | 00m00s [311/542] Installing adwaita-icon-theme 100% | 14.1 MiB/s | 2.4 MiB | 00m00s [312/542] Installing adwaita-cursor-the 100% | 158.7 MiB/s | 11.4 MiB | 00m00s [313/542] Installing adwaita-icon-theme 100% | 15.8 MiB/s | 1.3 MiB | 00m00s [314/542] Installing libepoxy-0:1.5.10- 100% | 216.4 MiB/s | 1.1 MiB | 00m00s [315/542] Installing hicolor-icon-theme 100% | 7.0 MiB/s | 179.5 KiB | 00m00s [316/542] Installing clang-resource-fil 100% | 16.3 MiB/s | 16.7 KiB | 00m00s [317/542] Installing qt6-filesystem-0:6 100% | 3.4 MiB/s | 3.5 KiB | 00m00s [318/542] Installing libdatrie-0:0.2.13 100% | 57.6 MiB/s | 58.9 KiB | 00m00s [319/542] Installing libthai-0:0.1.29-1 100% | 76.7 MiB/s | 785.2 KiB | 00m00s [320/542] Installing google-noto-fonts- 100% | 18.1 MiB/s | 18.5 KiB | 00m00s [321/542] Installing google-noto-sans-v 100% | 173.9 MiB/s | 1.4 MiB | 00m00s [322/542] Installing default-fonts-core 100% | 5.9 MiB/s | 18.2 KiB | 00m00s [323/542] Installing fontconfig-0:2.16. 100% | 718.3 KiB/s | 780.1 KiB | 00m01s [324/542] Installing libaribcaption-0:1 100% | 61.0 MiB/s | 249.9 KiB | 00m00s [325/542] Installing libbluray-0:1.3.4- 100% | 97.5 MiB/s | 399.2 KiB | 00m00s [326/542] Installing llvm-filesystem-0: 100% | 1.0 MiB/s | 1.1 KiB | 00m00s [327/542] Installing libedit-0:3.1-55.2 100% | 80.0 MiB/s | 245.8 KiB | 00m00s [328/542] Installing llvm-libs-0:20.1.6 100% | 98.0 MiB/s | 139.7 MiB | 00m01s [329/542] Installing clang-libs-0:20.1. 100% | 127.9 MiB/s | 118.7 MiB | 00m01s [330/542] Installing libwacom-data-0:2. 100% | 19.2 MiB/s | 1.5 MiB | 00m00s [331/542] Installing hwdata-0:0.395-1.f 100% | 175.6 MiB/s | 9.5 MiB | 00m00s [332/542] Installing libpciaccess-0:0.1 100% | 22.4 MiB/s | 45.9 KiB | 00m00s [333/542] Installing libdrm-0:2.4.124-2 100% | 100.5 MiB/s | 411.8 KiB | 00m00s [334/542] Installing libpciaccess-devel 100% | 15.5 MiB/s | 15.9 KiB | 00m00s [335/542] Installing libdrm-devel-0:2.4 100% | 58.4 MiB/s | 717.5 KiB | 00m00s [336/542] Installing lm_sensors-libs-0: 100% | 84.9 MiB/s | 86.9 KiB | 00m00s [337/542] Installing libxshmfence-0:1.3 100% | 13.2 MiB/s | 13.6 KiB | 00m00s [338/542] Installing mesa-dri-drivers-0 100% | 80.1 MiB/s | 45.8 MiB | 00m01s [339/542] Installing mesa-libgbm-0:25.1 100% | 20.0 MiB/s | 20.5 KiB | 00m00s [340/542] Installing mesa-libEGL-0:25.1 100% | 164.0 MiB/s | 335.9 KiB | 00m00s [341/542] Installing libglvnd-egl-1:1.7 100% | 34.3 MiB/s | 70.3 KiB | 00m00s [342/542] Installing libglvnd-gles-1:1. 100% | 104.8 MiB/s | 107.3 KiB | 00m00s [343/542] Installing libasyncns-0:0.8-3 100% | 59.3 MiB/s | 60.8 KiB | 00m00s [344/542] Installing 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python3-qt5-0:5.15 100% | 132.3 MiB/s | 6.0 MiB | 00m00s [497/542] Installing python3-olefile-0: 100% | 111.6 MiB/s | 343.0 KiB | 00m00s [498/542] Installing libevent-devel-0:2 100% | 22.2 MiB/s | 432.3 KiB | 00m00s [499/542] Installing avahi-devel-0:0.9~ 100% | 3.5 MiB/s | 135.8 KiB | 00m00s >>> Running sysusers scriptlet: unbound-libs-0:1.22.0-14.fc43.x86_64 >>> Finished sysusers scriptlet: unbound-libs-0:1.22.0-14.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'unbound' with GID 997. >>> Creating user 'unbound' (Unbound DNS resolver) with UID 997 and GID 997. >>> [500/542] Installing unbound-libs-0:1.2 100% | 130.9 MiB/s | 1.4 MiB | 00m00s [501/542] Installing gnutls-dane-0:3.8. 100% | 11.4 MiB/s | 70.2 KiB | 00m00s [502/542] Installing gnutls-devel-0:3.8 100% | 55.5 MiB/s | 5.8 MiB | 00m00s [503/542] Installing cups-devel-1:2.4.1 100% | 9.7 MiB/s | 189.0 KiB | 00m00s [504/542] Installing libzip-0:1.11.4-1. 100% | 66.9 MiB/s | 136.9 KiB | 00m00s [505/542] Installing netcdf-0:4.9.2-13. 100% | 60.3 MiB/s | 2.4 MiB | 00m00s [506/542] Installing libglvnd-core-deve 100% | 40.1 MiB/s | 41.1 KiB | 00m00s [507/542] Installing libglvnd-devel-1:1 100% | 163.1 MiB/s | 2.1 MiB | 00m00s [508/542] Installing mesa-libGLU-devel- 100% | 17.1 MiB/s | 17.5 KiB | 00m00s [509/542] Installing mesa-libGL-devel-0 100% | 9.9 MiB/s | 81.5 KiB | 00m00s [510/542] Installing qt5-qtbase-devel-0 100% | 43.1 MiB/s | 19.5 MiB | 00m00s [511/542] Installing libimagequant-0:4. 100% | 86.2 MiB/s | 705.9 KiB | 00m00s [512/542] Installing msgpack-0:3.1.0-18 100% | 11.2 MiB/s | 57.3 KiB | 00m00s [513/542] Installing msgpack-devel-0:3. 100% | 21.3 MiB/s | 5.2 MiB | 00m00s [514/542] Installing xz-devel-1:5.8.1-1 100% | 42.7 MiB/s | 262.6 KiB | 00m00s [515/542] Installing libxml2-devel-0:2. 100% | 24.8 MiB/s | 3.4 MiB | 00m00s [516/542] Installing libxkbcommon-devel 100% | 23.9 MiB/s | 367.5 KiB | 00m00s [517/542] Installing qt6-qtbase-devel-0 100% | 41.3 MiB/s | 21.5 MiB | 00m01s [518/542] Installing qt6-qtbase-private 100% | 46.0 MiB/s | 4.7 MiB | 00m00s [519/542] Installing qt6-qtdeclarative- 100% | 35.7 MiB/s | 23.5 MiB | 00m01s [520/542] Installing pyside6-tools-0:6. 100% | 6.6 MiB/s | 168.2 KiB | 00m00s [521/542] Installing freetype-devel-0:2 100% | 43.4 MiB/s | 8.5 MiB | 00m00s [522/542] Installing fontconfig-devel-0 100% | 10.9 MiB/s | 156.7 KiB | 00m00s [523/542] Installing cairo-devel-0:1.18 100% | 58.7 MiB/s | 2.3 MiB | 00m00s [524/542] Installing harfbuzz-devel-0:1 100% | 42.0 MiB/s | 5.4 MiB | 00m00s [525/542] Installing python3-pyside6-de 100% | 35.3 MiB/s | 2.9 MiB | 00m00s [526/542] Installing mmtf-cpp-devel-0:1 100% | 38.1 MiB/s | 117.0 KiB | 00m00s [527/542] Installing python3-pillow-0:1 100% | 46.6 MiB/s | 4.1 MiB | 00m00s [528/542] Installing python3-qt5-devel- 100% | 25.8 MiB/s | 2.8 MiB | 00m00s [529/542] Installing freeglut-devel-0:3 100% | 59.4 MiB/s | 2.3 MiB | 00m00s [530/542] Installing glew-devel-0:2.2.0 100% | 120.7 MiB/s | 1.8 MiB | 00m00s [531/542] Installing netcdf-devel-0:4.9 100% | 18.6 MiB/s | 380.1 KiB | 00m00s [532/542] Installing python3-pytest-0:8 100% | 44.8 MiB/s | 3.8 MiB | 00m00s [533/542] Installing python3-devel-0:3. 100% | 28.5 MiB/s | 1.8 MiB | 00m00s [534/542] Installing annobin-plugin-gcc 100% | 23.7 MiB/s | 995.2 KiB | 00m00s [535/542] Installing authselect-0:1.5.1 100% | 7.0 MiB/s | 158.2 KiB | 00m00s [536/542] Installing pam-0:1.7.0-4.fc42 100% | 34.6 MiB/s | 1.7 MiB | 00m00s [537/542] Installing gcc-plugin-annobin 100% | 1.4 MiB/s | 58.8 KiB | 00m00s [538/542] Installing desktop-file-utils 100% | 10.3 MiB/s | 222.2 KiB | 00m00s [539/542] Installing libappstream-glib- 100% | 48.8 MiB/s | 1.4 MiB | 00m00s [540/542] Installing glm-devel-0:1.0.1- 100% | 46.9 MiB/s | 2.2 MiB | 00m00s [541/542] Installing catch2-devel-0:2.1 100% | 134.0 MiB/s | 960.8 KiB | 00m00s [542/542] Installing systemd-rpm-macros 100% | 4.4 KiB/s | 8.9 KiB | 00m02s Warning: skipped OpenPGP checks for 24 packages from repository: copr_base Complete! Finish: build setup for pymol-3.1.0-7.fc43.src.rpm Start: rpmbuild pymol-3.1.0-7.fc43.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1748908800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.zRTKRZ Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.M4S4R0 + 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.KhThOe + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + FEDORA=43 + 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement not satisfied: numpy>=1.26.4,<3 Handling setuptools>=69.2.0 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-7.fc43.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 386.3 KiB/s | 10.0 KiB | 00m00s Copr repository 100% | 46.6 KiB/s | 1.5 KiB | 00m00s Coprdir repository 100% | 38.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "catch2-devel-2.13.10-6.fc42.x86_64" is already installed. Package "desktop-file-utils-0.28-1.fc43.x86_64" is already installed. Package "freeglut-devel-3.6.0-4.fc42.x86_64" is already installed. Package "freetype-devel-2.13.3-2.fc42.x86_64" is already installed. Package "gcc-15.1.1-2.fc43.x86_64" is already installed. Package "gcc-c++-15.1.1-2.fc43.x86_64" is already installed. Package "glew-devel-2.2.0-10.fc42.x86_64" is already installed. Package "glm-devel-1.0.1-4.fc43.noarch" is already installed. Package "mesa-libGL-devel-25.1.1-1.fc43.x86_64" is already installed. Package "libappstream-glib-0.8.3-3.fc42.x86_64" is already installed. Package "libpng-devel-2:1.6.48-1.fc43.x86_64" is already installed. Package "libxml2-devel-2.12.10-1.fc43.x86_64" is already installed. Package "mmtf-cpp-devel-1.1.0-7.fc42.x86_64" is already installed. Package "msgpack-devel-3.1.0-18.fc42.x86_64" is already installed. Package "netcdf-devel-4.9.2-13.fc43.x86_64" is already installed. Package "pyproject-rpm-macros-1.18.1-1.fc43.noarch" is already installed. Package "python3-devel-3.13.3-3.fc43.x86_64" is already installed. Package "python3-pillow-11.2.1-1.fc43.x86_64" is already installed. Package "python3-pyside6-devel-6.9.0-2.fc43.x86_64" is already installed. Package "python3-pytest-8.3.5-3.fc43.noarch" is already installed. Package "python3-qt5-devel-5.15.11-7.fc43.x86_64" is already installed. Package "python3-packaging-25.0-1.fc43.noarch" is already installed. Package Arch Version Repository Size Installing: python3-numpy x86_64 1:2.2.6-1.fc43 fedora 40.3 MiB python3-pip noarch 25.1.1-4.fc43 copr_base 11.5 MiB python3-setuptools noarch 78.1.1-1.fc43 fedora 8.6 MiB Installing dependencies: flexiblas x86_64 3.4.5-1.fc43 fedora 50.4 KiB flexiblas-netlib x86_64 3.4.5-1.fc43 fedora 10.9 MiB flexiblas-openblas-openmp x86_64 3.4.5-1.fc43 fedora 39.2 KiB openblas x86_64 0.3.29-1.fc42 fedora 111.7 KiB openblas-openmp x86_64 0.3.29-1.fc42 fedora 43.7 MiB python3-numpy-f2py x86_64 1:2.2.6-1.fc43 fedora 2.0 MiB Transaction Summary: Installing: 9 packages Total size of inbound packages is 22 MiB. Need to download 22 MiB. After this operation, 117 MiB extra will be used (install 117 MiB, remove 0 B). [1/9] python3-pip-0:25.1.1-4.fc43.noarc 100% | 20.5 MiB/s | 2.5 MiB | 00m00s [2/9] python3-setuptools-0:78.1.1-1.fc4 100% | 6.6 MiB/s | 2.0 MiB | 00m00s [3/9] python3-numpy-f2py-1:2.2.6-1.fc43 100% | 10.0 MiB/s | 492.6 KiB | 00m00s [4/9] flexiblas-0:3.4.5-1.fc43.x86_64 100% | 570.5 KiB/s | 26.2 KiB | 00m00s [5/9] python3-numpy-1:2.2.6-1.fc43.x86_ 100% | 18.3 MiB/s | 8.1 MiB | 00m00s [6/9] flexiblas-openblas-openmp-0:3.4.5 100% | 221.2 KiB/s | 17.3 KiB | 00m00s [7/9] flexiblas-netlib-0:3.4.5-1.fc43.x 100% | 9.1 MiB/s | 3.4 MiB | 00m00s [8/9] openblas-0:0.3.29-1.fc42.x86_64 100% | 1.4 MiB/s | 42.3 KiB | 00m00s [9/9] openblas-openmp-0:0.3.29-1.fc42.x 100% | 28.7 MiB/s | 5.4 MiB | 00m00s -------------------------------------------------------------------------------- [9/9] Total 100% | 33.2 MiB/s | 21.9 MiB | 00m01s Running transaction [ 1/11] Verify package files 100% | 230.0 B/s | 9.0 B | 00m00s [ 2/11] Prepare transaction 100% | 50.0 B/s | 9.0 B | 00m00s [ 3/11] Installing openblas-0:0.3.29-1. 100% | 55.4 MiB/s | 113.5 KiB | 00m00s [ 4/11] Installing openblas-openmp-0:0. 100% | 273.2 MiB/s | 43.7 MiB | 00m00s [ 5/11] Installing flexiblas-netlib-0:3 100% | 145.8 MiB/s | 10.9 MiB | 00m00s [ 6/11] Installing flexiblas-0:3.4.5-1. 100% | 50.4 MiB/s | 51.6 KiB | 00m00s [ 7/11] Installing flexiblas-openblas-o 100% | 7.8 MiB/s | 40.1 KiB | 00m00s [ 8/11] Installing python3-numpy-1:2.2. 100% | 74.0 MiB/s | 40.6 MiB | 00m01s [ 9/11] Installing python3-numpy-f2py-1 100% | 35.1 MiB/s | 2.1 MiB | 00m00s [10/11] Installing python3-setuptools-0 100% | 56.2 MiB/s | 8.8 MiB | 00m00s [11/11] Installing python3-pip-0:25.1.1 100% | 38.4 MiB/s | 11.8 MiB | 00m00s Warning: skipped OpenPGP checks for 1 package from repository: copr_base Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1748908800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.vOK7d7 + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + FEDORA=43 + 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.6) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 78.1.1) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.6) 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-7.fc43.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 287.0 KiB/s | 10.0 KiB | 00m00s Copr repository 100% | 43.9 KiB/s | 1.5 KiB | 00m00s Coprdir repository 100% | 37.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Nothing to do. Package "catch2-devel-2.13.10-6.fc42.x86_64" is already installed. Package "desktop-file-utils-0.28-1.fc43.x86_64" is already installed. Package "freeglut-devel-3.6.0-4.fc42.x86_64" is already installed. Package "freetype-devel-2.13.3-2.fc42.x86_64" is already installed. Package "gcc-15.1.1-2.fc43.x86_64" is already installed. Package "gcc-c++-15.1.1-2.fc43.x86_64" is already installed. Package "glew-devel-2.2.0-10.fc42.x86_64" is already installed. Package "glm-devel-1.0.1-4.fc43.noarch" is already installed. Package "mesa-libGL-devel-25.1.1-1.fc43.x86_64" is already installed. Package "libappstream-glib-0.8.3-3.fc42.x86_64" is already installed. Package "libpng-devel-2:1.6.48-1.fc43.x86_64" is already installed. Package "libxml2-devel-2.12.10-1.fc43.x86_64" is already installed. Package "mmtf-cpp-devel-1.1.0-7.fc42.x86_64" is already installed. Package "msgpack-devel-3.1.0-18.fc42.x86_64" is already installed. Package "netcdf-devel-4.9.2-13.fc43.x86_64" is already installed. Package "pyproject-rpm-macros-1.18.1-1.fc43.noarch" is already installed. Package "python3-devel-3.13.3-3.fc43.x86_64" is already installed. Package "python3-pillow-11.2.1-1.fc43.x86_64" is already installed. Package "python3-pyside6-devel-6.9.0-2.fc43.x86_64" is already installed. Package "python3-pytest-8.3.5-3.fc43.noarch" is already installed. Package "python3-qt5-devel-5.15.11-7.fc43.x86_64" is already installed. Package "python3-packaging-25.0-1.fc43.noarch" is already installed. Package "python3-pip-25.1.1-4.fc43.noarch" is already installed. Package "python3-setuptools-78.1.1-1.fc43.noarch" is already installed. Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1748908800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.AqMWey + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/.pyproject-builddir + RPM_TOXENV=py313 + FEDORA=43 + 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.6) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 78.1.1) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.2.6) 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-3.1.0-7.fc43.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.GdWu7d + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 + mkdir -p /builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/pymol-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) /usr/lib/python3.13/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2026-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) 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-x86_64-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/Pick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-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-x86_64-linux-gnu.so -- The C compiler identification is GNU 15.1.1 -- The CXX compiler identification is GNU 15.1.1 -- 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 (0.0s) -- Build files have been written to: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-313/_cmd cmake --build . --config Release -j2 /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-x86_64-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-x86_64-cpython-313/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-cpython-313/_cmd' /usr/bin/gmake -f CMakeFiles/_cmd.dir/build.make CMakeFiles/_cmd.dir/depend gmake[2]: Entering directory 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-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 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-D_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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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; | ^~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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() { | ^~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~ 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/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); | ^ /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); | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ‘sprintf’, 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_chk’ output between 2 and 12 bytes into a destination of size 8 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.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 ‘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; | ^~~~~~~~~~ [ 5%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp [ 6%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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/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 | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) { | ^~~~~~~~~~~~~ /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) { | ^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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]; | ^~~~ /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/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, | ^ /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] /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); | ^ /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/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_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)); | ^ /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)); | ^ /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); | ^ [ 9%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 ‘sprintf’, 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_chk’ output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-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 ‘sprintf’, 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_chk’ output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 675 | sprintf(answer, "%03x/", d1); | ^ In function ‘sprintf’, inlined from ‘DDreldir(std::__cxx11::basic_string, std::allocator > const&, int, int)’ at /builddir/build/BUILD/pymol-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_chk’ output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-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 ‘sprintf’, 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_chk’ output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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) { | ^~~~~~~~~~~~~~~ /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); | ^ [ 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 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-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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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) { | ^~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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; | ^~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) | ^~~~~~~~~~~~~ /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)); | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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); | ~~~~~^~~~~~~~~~~~~~~~~~ /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(), | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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, | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) { | ^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^ /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); | ^ /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); | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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; | ^~~~ 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/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/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 ‘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; | ^ /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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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) { | ^~~~~~~~~~~~~~~ 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/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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /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; | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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; | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ~~~~~^~~~~~~~~~~~~~~~~~ /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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ^~~~~~~~~~~~~~~ /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) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 22%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c.o /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) | ^~~~~~~~~~~~~~~~~~~~~~ /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) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) { | ^~~~~~~~~~~~~~~~~~~~~~~ /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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o -MF CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o.d -o CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.o -c /builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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/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/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 ‘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); | ^ [ 25%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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/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); | ^ /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); | ^ /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); | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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) { | ^~~~~~~~~~~~~~~~~~~~~~~ /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)); | ^ [ 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 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-fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 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-Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 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-mno-omit-leaf-frame-pointer -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 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/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 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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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/File.cpp.o -MF CMakeFiles/_cmd.dir/layer0/File.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/File.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/File.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; | ~~~~~~~~~~^~~~~~~ [ 30%] Building CXX object CMakeFiles/_cmd.dir/layer0/GFXManager.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o -MF CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/MemoryDebug.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.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/MemoryUsage.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MyPNG.cpp:342:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 342 | for(a = 0; a < width; a++) { | ~~^~~~~~~ [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/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 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-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type 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-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 35%] Building CXX object CMakeFiles/_cmd.dir/layer0/PrintUtils.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include 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-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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, | ^~~~~~~~~~ [ 36%] Building CXX object 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -D_HAVE_LIBXML -D_PYMOL_CTEST -D_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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 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/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 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-mno-omit-leaf-frame-pointer -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 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -D_HAVE_LIBXML -D_PYMOL_CTEST -D_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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o -MF CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/ccealignmodule.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ccealignmodule.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; | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ~~^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt.h:45: In member function ‘TNT::Array1D::set_(double*, double*, double const&)’, inlined from ‘TNT::Array1D::Array1D(int, double const&)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:119:6, inlined from ‘findBest(cePoint*, cePoint*, afp**, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:506:28: [ 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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o -MF CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/os_gl.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/os_gl.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:283:20: warning: ‘memset’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 283 | *p = a; | ~~~^~~ [ 41%] Building CXX object CMakeFiles/_cmd.dir/layer1/Basis.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/Basis.cpp.o -MF CMakeFiles/_cmd.dir/layer1/Basis.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/Basis.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Basis.cpp [ 42%] Building CXX object CMakeFiles/_cmd.dir/layer1/ButMode.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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); | ^~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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, | ^~~~~~~~~~ /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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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()) { | ~~~~~~^~~~~~~~~~~~~~~ /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) { | ~~^~~~~~~ /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) { | ~~^~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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; | ^~~~~~~~~~ [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o /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/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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); | ^~~~~~~ [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Font.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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: ‘MEM [(float *)_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:744:13: warning: ‘MEM[(float *)_62 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 744 | *(v1++) = *(v++); | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp: In function ‘ExtrudeCGOSurfaceTube(CExtrude const*, CGO*, cCylCap, float const*, bool, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp:949:46: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 949 | if(color_override && (b > start) && (b < stop)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp:876:14: note: ‘stop’ was declared here 876 | int start, stop; | ^~~~ 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 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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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontGLUTHel12.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUTHel12.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUTHel12.cpp.o -c 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-mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontGLUTHel18.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUTHel18.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUTHel18.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUTHel18.cpp [ 48%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontType.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/FontType.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontType.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontType.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontType.cpp [ 49%] Building CXX object CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ImageUtils.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ImageUtils.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, | ^~~~~~~~~~ [ 49%] Building CXX object CMakeFiles/_cmd.dir/layer1/Movie.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ /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/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/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) | ^~~~~~~~~~~~ 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)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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/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/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: 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 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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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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++) { | ~~^~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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++) { | ~~^~~~~~~~~~~~~~~~ /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; | ^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /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:4444, 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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~ 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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o -MF CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/ScrollBar.cpp.o -c /builddir/build/BUILD/pymol-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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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/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) | ^~~~~~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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); | ^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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:4444, 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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 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-mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 CMakeFiles/_cmd.dir/layer1/Text.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Text.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/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, | ^~~~~~~~~~ [ 58%] Building CXX object CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST 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-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o -MF CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/TypeFace.cpp [ 59%] Building CXX object CMakeFiles/_cmd.dir/layer1/View.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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); | ^~~~~~~ [ 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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o -MF CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/AtomInfo.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfo.cpp [ 60%] Building CXX object CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o -MF CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/AtomInfoHistory.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/AtomInfoHistory.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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ [ 60%] Building CXX object CMakeFiles/_cmd.dir/layer2/BondTypeHistory.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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] [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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/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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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()) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ~~~~^~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp: In member function ‘ObjectAlignment::update()’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:918:39: warning: ‘MEM[(float *)&gvert]’ may be used uninitialized [-Wmaybe-uninitialized] 918 | float mean[3], vert[3], gvert[3]; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:918:39: warning: ‘MEM[(float *)&gvert + 4B]’ may be used uninitialized [-Wmaybe-uninitialized] /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:975:25: warning: ‘MEM[(float *)&first]’ may be used uninitialized [-Wmaybe-uninitialized] 975 | float first[3]; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectAlignment.cpp:975:25: warning: ‘MEM[(float *)&first + 4B]’ may be used uninitialized [-Wmaybe-uninitialized] [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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, | ^~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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( | ^~~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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/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, | ^~~~~~~~~~ /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: ‘snprintf’ 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: ‘snprintf’ 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/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: ‘snprintf’ output 31 or more bytes (assuming 286) 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/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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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 ‘snprintf’, 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_chk’ 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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ 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/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 ‘int’ [-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) { | ~~~~~^~~~~~~~~~~ /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/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 ‘snprintf’, 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_chk’ 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 ‘snprintf’, 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: /usr/include/bits/stdio2.h:68:35: note: ‘__snprintf_chk’ 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 ‘snprintf’, 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_chk’ 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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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: ‘snprintf’ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/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/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: ‘snprintf’ output between 68 and 333 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 ‘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: ‘sprintf’ output between 78 and 2036 bytes into a destination of size 1024 10749 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10750 | buffer, v[0], v[1], v[2], state + 1, mode, 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ‘snprintf’, inlined from ‘ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, char const*, char const*, char const*, char const*, char const*, char const*, float, int, float, float, char const*, float const*, int, int, int, int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule2.cpp:334:7: /usr/include/bits/stdio2.h:68:35: note: ‘__snprintf_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) { | ~~~~^~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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, | ^~~~~~~~~~ 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/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/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/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: ‘snprintf’ 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: ‘snprintf’ output between 28 and 283 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/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: ‘snprintf’ output 34 or more bytes (assuming 289) into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 70%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectVolume.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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: ‘snprintf’ output between 30 and 285 bytes 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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++) { | ~~^~~~~~~~~~~~~~~~~ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~ /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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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, | ^~~~~~~~~~ /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; | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ 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 /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; | ^~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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/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, | ^~~~~~~~~~ /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: ‘MEM [(float *)_706]’ 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:424:15: warning: ‘MEM[(float *)_706 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 424 | *(v1++) = *(v++); | ^~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ /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) { | ~~^~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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-mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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; | ^~~~~~ 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/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: ‘snprintf’ output between 22 and 277 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/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: ‘sprintf’ 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: ‘sprintf’ 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: ‘sprintf’ 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/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) { | ^~ | & 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) | ^~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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) { | ~~^~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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; | ^~~~~ /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: ‘snprintf’ 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: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 38 and 556 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 42 or more bytes (assuming 306) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 44 and 562 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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++) { | ~~^~~~~~~~~~~~~~~~~ /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: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 43 and 1338 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 34 and 1320 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ 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: ‘snprintf’ 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: ‘snprintf’ output between 84 and 339 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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: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: ‘snprintf’ output between 49 and 314 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: ‘snprintf’ 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: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: ‘snprintf’ output between 35 and 300 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/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, | ^~~~~~~~~~ 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; | ^~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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: ‘snprintf’ output 42 or more bytes (assuming 297) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 43 or more bytes (assuming 1084) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 34 or more bytes (assuming 1066) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 43 or more bytes (assuming 1330) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 34 or more bytes (assuming 1312) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 21 or more bytes (assuming 1044) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 44 or more bytes (assuming 299) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 41 or more bytes (assuming 305) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-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: ‘snprintf’ output 32 or more bytes (assuming 287) into a destination of size 255 282 | #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ In file included from /builddir/build/BUILD/pymol-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, | ^~~~~~~~~~ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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: ‘sprintf’ output between 32 and 1057 bytes into a destination of size 1024 15625 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 15626 | order_input, (location == -2) ? "upper" : "current"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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: ‘snprintf’ 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: ‘snprintf’ 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/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: ‘snprintf’ 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: ‘snprintf’ 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: ‘snprintf’ 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: ‘snprintf’ output between 49 and 304 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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/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 ‘snprintf’, 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_chk’ 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 /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) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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, | ^~~~~~~~~~ /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); | ^~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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/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:4444, 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 ‘snprintf’, 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_chk’ 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/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) { | ~~^~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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); | ^~~~~~~ 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, | ^~~~~~~~~~ /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); | ^~~~~~~ [ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp -MD -MT CMakeFiles/_cmd.dir/layer5/main.cpp.o -MF CMakeFiles/_cmd.dir/layer5/main.cpp.o.d -o CMakeFiles/_cmd.dir/layer5/main.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/main.cpp [ 88%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS 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/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; | ^~~~~~~~ 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 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 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CMakeFiles/_cmd.dir/layer2/Sculpt.cpp.o CMakeFiles/_cmd.dir/layer2/SculptCache.cpp.o CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o CMakeFiles/_cmd.dir/layer2/VFont.cpp.o CMakeFiles/_cmd.dir/layer3/AtomIterators.cpp.o CMakeFiles/_cmd/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); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveManageObject’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14627:11: warning: ‘strcpy’ writing between 1 and 256 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 14627 | strcpy(rec->name, obj->Name); | ^ lto1: note: destination object is likely at address zero In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes into a region of size 4 [-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: destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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 [8, 12] into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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 [16, 20] into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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 [24, 28] into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 4 bytes 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 /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 /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: /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 4 bytes 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 [8, 12] 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 8 into destination object ‘nx’ of size 4 /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 [8, 12] into destination object ‘nx’ of size 4 /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 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_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 4 bytes 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 [12, 16] 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 12 into destination object ‘nx’ of size 4 /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 [12, 16] into destination object ‘nx’ of size 4 /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 12 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: /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 4 bytes 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 [16, 20] 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 16 into destination object ‘nx’ of size 4 /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 [16, 20] into destination object ‘nx’ of size 4 /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 16 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: /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 4 bytes 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 [20, 24] 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 20 into destination object ‘nx’ of size 4 /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 [20, 24] into destination object ‘nx’ of size 4 /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 20 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: /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 4 bytes 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 [24, 28] 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 24 into destination object ‘nx’ of size 4 /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 [24, 28] into destination object ‘nx’ of size 4 /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 24 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: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 8 bytes into a region of size 4 [-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: destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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; | ^ 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 8 bytes 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 [16, 20] into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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 [24, 28] into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 4 bytes 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 /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 /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 4 bytes 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 /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 /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: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 4 bytes 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 [12, 16] 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 12 into destination object ‘ny’ of size 4 /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 [12, 16] into destination object ‘ny’ of size 4 /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 12 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 4 bytes 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 [16, 20] 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 16 into destination object ‘ny’ of size 4 /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 [16, 20] into destination object ‘ny’ of size 4 /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 16 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 4 bytes 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 [20, 24] 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 20 into destination object ‘ny’ of size 4 /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 [20, 24] into destination object ‘ny’ of size 4 /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 20 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 4 bytes 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 [24, 28] 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 24 into destination object ‘ny’ of size 4 /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 [24, 28] into destination object ‘ny’ of size 4 /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 24 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 8 bytes into a region of size 4 [-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: destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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; | ^ 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 8 bytes 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 [16, 20] into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 8 bytes 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 [24, 28] into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ In function ‘swap4_unaligned’, inlined from ‘get_float’ at /builddir/build/BUILD/pymol-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 4 bytes 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 /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 /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 4 bytes 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 /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 /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_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 4 bytes 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 [12, 16] 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 12 into destination object ‘nz’ of size 4 /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 [12, 16] into destination object ‘nz’ of size 4 /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 12 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 4 bytes 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 [16, 20] 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 16 into destination object ‘nz’ of size 4 /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 [16, 20] into destination object ‘nz’ of size 4 /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 16 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 4 bytes 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 [20, 24] 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 20 into destination object ‘nz’ of size 4 /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 [20, 24] into destination object ‘nz’ of size 4 /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 20 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 4 bytes 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 [24, 28] 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 24 into destination object ‘nz’ of size 4 /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 [24, 28] into destination object ‘nz’ of size 4 /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 24 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 8 bytes into a region of size 4 [-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: destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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; | ^ 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 8 bytes 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 [16, 20] into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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 [24, 28] into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 4 bytes 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 /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 /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 4 bytes 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 /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 /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: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 4 bytes 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 [12, 16] 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 12 into destination object ‘nx’ of size 4 /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 [12, 16] into destination object ‘nx’ of size 4 /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 12 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 4 bytes 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 [16, 20] 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 16 into destination object ‘nx’ of size 4 /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 [16, 20] into destination object ‘nx’ of size 4 /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 16 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 4 bytes 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 [20, 24] 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 20 into destination object ‘nx’ of size 4 /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 [20, 24] into destination object ‘nx’ of size 4 /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 20 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 4 bytes 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 [24, 28] 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 24 into destination object ‘nx’ of size 4 /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 [24, 28] into destination object ‘nx’ of size 4 /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 24 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 8 bytes into a region of size 4 [-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: destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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; | ^ 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 8 bytes 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 [16, 20] into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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 [24, 28] into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 4 bytes 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 /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 /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 4 bytes 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 /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 /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: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 4 bytes 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 [12, 16] 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 12 into destination object ‘ny’ of size 4 /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 [12, 16] into destination object ‘ny’ of size 4 /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 12 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 4 bytes 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 [16, 20] 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 16 into destination object ‘ny’ of size 4 /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 [16, 20] into destination object ‘ny’ of size 4 /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 16 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 4 bytes 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 [20, 24] 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 20 into destination object ‘ny’ of size 4 /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 [20, 24] into destination object ‘ny’ of size 4 /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 20 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 4 bytes 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 [24, 28] 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 24 into destination object ‘ny’ of size 4 /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 [24, 28] into destination object ‘ny’ of size 4 /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 24 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 8 bytes into a region of size 4 [-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: destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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 destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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 [16, 20] into destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 8 bytes 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 [24, 28] into destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ 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 4 bytes 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 /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 /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 4 bytes 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 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 8 into destination object ‘nz’ of size 4 /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 destination object ‘nz’ of size 4 /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 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 4 bytes 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 [12, 16] 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 12 into destination object ‘nz’ of size 4 /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 [12, 16] into destination object ‘nz’ of size 4 /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 12 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 4 bytes 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 [16, 20] 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 16 into destination object ‘nz’ of size 4 /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 [16, 20] into destination object ‘nz’ of size 4 /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 16 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 4 bytes 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 [20, 24] 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 20 into destination object ‘nz’ of size 4 /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 [20, 24] into destination object ‘nz’ of size 4 /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 20 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 4 bytes 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 [24, 28] 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 24 into destination object ‘nz’ of size 4 /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 [24, 28] into destination object ‘nz’ of size 4 /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 24 into destination object ‘nz’ of size 4 In member function ‘set_’, inlined from ‘__ct ’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:119:6, inlined from ‘findBest’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ccealignmodule.cpp:506:28: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include/tnt/tnt_array1d.h:283:20: warning: ‘__builtin_memset’ specified bound between 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-mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/os_memory.c.o -MF CMakeFiles/_champ.dir/contrib/champ/os_memory.c.o.d -o CMakeFiles/_champ.dir/contrib/champ/os_memory.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/os_memory.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/os_memory.c: In function ‘OSMemoryZero’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/os_memory.c:55:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 55 | while(count&&(((int)p)&mask)) { | ^ [ 72%] Building C object CMakeFiles/_champ.dir/contrib/champ/sort.c.o /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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/sort.c.o -MF CMakeFiles/_champ.dir/contrib/champ/sort.c.o.d -o CMakeFiles/_champ.dir/contrib/champ/sort.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/sort.c [ 81%] Building C object CMakeFiles/_champ.dir/contrib/champ/strblock.c.o /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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/strblock.c.o -MF CMakeFiles/_champ.dir/contrib/champ/strblock.c.o.d -o CMakeFiles/_champ.dir/contrib/champ/strblock.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/strblock.c [ 90%] Building C object CMakeFiles/_champ.dir/contrib/champ/vla.c.o /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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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-x86_64-cpython-313/chempy/champ/_champ.cpython-313-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/_champ.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,_champ.cpython-313-x86_64-linux-gnu.so -o /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/lib.linux-x86_64-cpython-313/chempy/champ/_champ.cpython-313-x86_64-linux-gnu.so CMakeFiles/_champ.dir/contrib/champ/champ.c.o CMakeFiles/_champ.dir/contrib/champ/champ_module.c.o CMakeFiles/_champ.dir/contrib/champ/chiral.c.o CMakeFiles/_champ.dir/contrib/champ/err2.c.o CMakeFiles/_champ.dir/contrib/champ/feedback2.c.o CMakeFiles/_champ.dir/contrib/champ/list.c.o CMakeFiles/_champ.dir/contrib/champ/os_memory.c.o CMakeFiles/_champ.dir/contrib/champ/sort.c.o CMakeFiles/_champ.dir/contrib/champ/strblock.c.o CMakeFiles/_champ.dir/contrib/champ/vla.c.o gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-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-x86_64-cpython-313/_champ/CMakeFiles 0 running bdist_wheel running build running build_py copying modules/chempy/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-cpython-313/chempy copying modules/chempy/xyz.py -> build/lib.linux-x86_64-cpython-313/chempy creating build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/scene_bin_gui.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/shortcut_menu_gui.py -> build/lib.linux-x86_64-cpython-313/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-x86_64-cpython-313/pmg_qt creating build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-x86_64-cpython-313/pmg_tk copying modules/pymol/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/__main__.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/_gui.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/cgobuilder.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/lazyio.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/morphing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/mpeg_encode.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/save_shortcut.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/seqalign.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/shortcut_dict.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/shortcut_manager.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-cpython-313/pymol copying modules/pymol/xwin.py -> build/lib.linux-x86_64-cpython-313/pymol creating build/lib.linux-x86_64-cpython-313/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-x86_64-cpython-313/pymol2 creating build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-cpython-313/chempy/bmin copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-cpython-313/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-cpython-313/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-cpython-313/chempy/champ creating build/lib.linux-x86_64-cpython-313/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/fast creating build/lib.linux-x86_64-cpython-313/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/fragments creating build/lib.linux-x86_64-cpython-313/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-x86_64-cpython-313/chempy/mmtf creating build/lib.linux-x86_64-cpython-313/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-cpython-313/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-cpython-313/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-cpython-313/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-cpython-313/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-cpython-313/chempy/tinker creating build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms creating build/lib.linux-x86_64-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-x86_64-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-x86_64-cpython-313/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-x86_64-cpython-313/pmg_qt/syntax creating build/lib.linux-x86_64-cpython-313/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/skins creating build/lib.linux-x86_64-cpython-313/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/startup creating build/lib.linux-x86_64-cpython-313/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/skins/demo creating build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal creating build/lib.linux-x86_64-cpython-313/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-x86_64-cpython-313/pymol/Qt creating build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-x86_64-cpython-313/pymol/plugins creating build/lib.linux-x86_64-cpython-313/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol/stereochemistry creating build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-cpython-313/pymol/wizard creating build/lib.linux-x86_64-cpython-313/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-x86_64-cpython-313/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-x86_64-cpython-313/web/examples creating build/lib.linux-x86_64-cpython-313/pymol_web/examples copying modules/pymol_web/examples/__init__.py -> build/lib.linux-x86_64-cpython-313/pymol_web/examples copying modules/pymol_web/examples/justhttpd.py -> build/lib.linux-x86_64-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:163: 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-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/change_confirm.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/create_shortcut.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/help_shortcut.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-x86_64-cpython-313/pmg_qt/forms copying modules/pmg_qt/forms/shortcut_menu.ui -> build/lib.linux-x86_64-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-x86_64-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-x86_64-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-x86_64-cpython-313/_cmd cmake --build . --config Release -j2 /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-x86_64-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-x86_64-cpython-313/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-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-x86_64-cpython-313/_cmd' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-313/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-cpython-313/_champ cmake --build . --config Release -j2 /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-x86_64-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-x86_64-cpython-313/_champ/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-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-x86_64-cpython-313/_champ' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-cpython-313/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-313/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-cpython-313/_champ/CMakeFiles 0 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/pymol copying build/lib.linux-x86_64-cpython-313/pymol/_cmd.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/__main__.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/_gui.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/api.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/callback.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/cgo.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/cgobuilder.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/checking.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/cmd.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/colorprinting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/colorramping.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/commanding.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/completing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/computing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/constants.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/constants_palette.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/controlling.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/creating.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/diagnosing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/editing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/editor.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/experimenting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/exporting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/externing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/feedingback.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/fitting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/gui.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/headering.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/helping.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/importing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/internal.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/invocation.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/keyboard.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/keywords.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/lazyio.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/locking.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/menu.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/monitoring.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/morphing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/movie.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/moving.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/mpeg_encode.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/parser.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/parsing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/povray.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/preset.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/pymolhttpd.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/querying.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/rpc.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/save_shortcut.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/selecting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/selector.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/seqalign.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/setting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/shortcut.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/shortcut_dict.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/shortcut_manager.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/util.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/vfont.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/viewing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/wizarding.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/xray.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-313/pymol/xwin.py -> build/bdist.linux-x86_64/wheel/./pymol creating build/bdist.linux-x86_64/wheel/pymol/Qt copying build/lib.linux-x86_64-cpython-313/pymol/Qt/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/Qt copying build/lib.linux-x86_64-cpython-313/pymol/Qt/utils.py -> build/bdist.linux-x86_64/wheel/./pymol/Qt creating build/bdist.linux-x86_64/wheel/pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/installation.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/legacysupport.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/managergui.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/managergui_qt.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-313/pymol/plugins/repository.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins creating build/bdist.linux-x86_64/wheel/pymol/stereochemistry copying build/lib.linux-x86_64-cpython-313/pymol/stereochemistry/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/stereochemistry creating build/bdist.linux-x86_64/wheel/pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/annotation.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/appearance.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/benchmark.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/box.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/charge.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/cleanup.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/command.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/demo.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/density.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/distance.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/dragging.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/filter.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/label.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/measurement.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/message.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/mutagenesis.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/nucmutagenesis.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/openvr.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/pair_fit.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/pseudoatom.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/renaming.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/sculpting.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/security.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/stereodemo.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-313/pymol/wizard/toggle.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard creating build/bdist.linux-x86_64/wheel/chempy creating build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/champ/_champ.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/champ/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/champ/amber99.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/champ/assign.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/champ/formal_charges.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-313/chempy/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/arc.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/bond_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/bond_mmff.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/bonds.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/brick.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/cc1.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/charge.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/cif.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/cpv.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/dictdb.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/gamess1.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/gms.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/hetatm.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/io.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/lst.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/mae.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/map.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/mass.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/mmd.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/models.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/mol.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/mol2.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/neighbor.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/pdb.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/pkl.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/place.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/protein.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/protein_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/protein_amber99.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/protein_mmff.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/protein_residues.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/sdf.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/solvate.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/water_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/water_residues.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-313/chempy/xyz.py -> build/bdist.linux-x86_64/wheel/./chempy creating build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-313/chempy/bmin/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-313/chempy/bmin/commands.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-313/chempy/bmin/realtime.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-313/chempy/bmin/state.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-313/chempy/bmin/util.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin creating build/bdist.linux-x86_64/wheel/chempy/fast copying build/lib.linux-x86_64-cpython-313/chempy/fast/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/fast creating build/bdist.linux-x86_64/wheel/chempy/fragments copying build/lib.linux-x86_64-cpython-313/chempy/fragments/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/fragments creating build/bdist.linux-x86_64/wheel/chempy/mmtf copying build/lib.linux-x86_64-cpython-313/chempy/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/mmtf copying build/lib.linux-x86_64-cpython-313/chempy/mmtf/io.py -> build/bdist.linux-x86_64/wheel/./chempy/mmtf creating build/bdist.linux-x86_64/wheel/chempy/tinker copying build/lib.linux-x86_64-cpython-313/chempy/tinker/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-313/chempy/tinker/amber.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-313/chempy/tinker/keyword.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-313/chempy/tinker/realtime.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-313/chempy/tinker/state.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker creating build/bdist.linux-x86_64/wheel/pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/TextEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/advanced_settings_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/builder.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/file_dialogs.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/keymapping.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/mimic_pmg_tk.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/mimic_tk.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/properties_dialog.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/pymol_gl_widget.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/pymol_qt_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/scene_bin_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/shortcut_menu_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-313/pmg_qt/volume.py -> build/bdist.linux-x86_64/wheel/./pmg_qt creating build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/askpartial.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/change_confirm.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/colors.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/create_shortcut.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/fetch.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/help_shortcut.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/load_aln.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/load_mae.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/load_map.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/load_mtz.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/load_traj.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/movieexport.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/pluginitem.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/pluginmanager.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/png.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/props.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/render.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/save_molecule.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/save_object.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-313/pmg_qt/forms/shortcut_menu.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms creating build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-313/pmg_qt/syntax/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-313/pmg_qt/syntax/pml.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-313/pmg_qt/syntax/pmlparser.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-313/pmg_qt/syntax/python.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax creating build/bdist.linux-x86_64/wheel/pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/ColorEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/Demo.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/PMGApp.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/PyMOLMapLoad.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/SetEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/Setting.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/TextEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-313/pmg_tk/volume.py -> build/bdist.linux-x86_64/wheel/./pmg_tk creating build/bdist.linux-x86_64/wheel/pmg_tk/skins copying build/lib.linux-x86_64-cpython-313/pmg_tk/skins/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins creating build/bdist.linux-x86_64/wheel/pmg_tk/skins/demo copying build/lib.linux-x86_64-cpython-313/pmg_tk/skins/demo/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/demo creating build/bdist.linux-x86_64/wheel/pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal/ModalWindow.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-313/pmg_tk/skins/normal/builder.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal creating build/bdist.linux-x86_64/wheel/pmg_tk/startup copying build/lib.linux-x86_64-cpython-313/pmg_tk/startup/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/startup creating build/bdist.linux-x86_64/wheel/pymol2 copying build/lib.linux-x86_64-cpython-313/pymol2/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol2 copying build/lib.linux-x86_64-cpython-313/pymol2/cmd2.py -> build/bdist.linux-x86_64/wheel/./pymol2 creating build/bdist.linux-x86_64/wheel/web creating build/bdist.linux-x86_64/wheel/web/examples copying build/lib.linux-x86_64-cpython-313/web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./web/examples copying build/lib.linux-x86_64-cpython-313/web/examples/justhttpd.py -> build/bdist.linux-x86_64/wheel/./web/examples creating build/bdist.linux-x86_64/wheel/pymol_web creating build/bdist.linux-x86_64/wheel/pymol_web/examples copying build/lib.linux-x86_64-cpython-313/pymol_web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol_web/examples copying build/lib.linux-x86_64-cpython-313/pymol_web/examples/justhttpd.py -> build/bdist.linux-x86_64/wheel/./pymol_web/examples running install_egg_info Copying modules/pymol.egg-info to build/bdist.linux-x86_64/wheel/./pymol-3.1.0-py3.13.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pymol/pymol_path copying LICENSE -> build/bdist.linux-x86_64/wheel/./pymol/pymol_path copying data -> build/bdist.linux-x86_64/wheel/./pymol/pymol_path/data copying test -> build/bdist.linux-x86_64/wheel/./pymol/pymol_path/test copying examples -> build/bdist.linux-x86_64/wheel/./pymol/pymol_path/examples creating build/bdist.linux-x86_64/wheel/pymol-3.1.0.data/scripts creating build/bdist.linux-x86_64/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-sizu70kn/.tmp-4x0iq_e7/pymol-3.1.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'chempy/__init__.py' adding 'chempy/arc.py' adding 'chempy/bond_amber.py' adding 'chempy/bond_mmff.py' adding 'chempy/bonds.py' adding 'chempy/brick.py' adding 'chempy/cc1.py' adding 'chempy/charge.py' adding 'chempy/cif.py' adding 'chempy/cpv.py' adding 'chempy/dictdb.py' adding 'chempy/gamess1.py' adding 'chempy/gms.py' adding 'chempy/hetatm.py' adding 'chempy/io.py' adding 'chempy/lst.py' adding 'chempy/mae.py' adding 'chempy/map.py' adding 'chempy/mass.py' adding 'chempy/mmd.py' adding 'chempy/models.py' adding 'chempy/mol.py' adding 'chempy/mol2.py' adding 'chempy/neighbor.py' adding 'chempy/pdb.py' adding 'chempy/pkl.py' adding 'chempy/place.py' adding 'chempy/protein.py' adding 'chempy/protein_amber.py' adding 'chempy/protein_amber99.py' adding 'chempy/protein_mmff.py' adding 'chempy/protein_residues.py' adding 'chempy/sdf.py' adding 'chempy/solvate.py' adding 'chempy/water_amber.py' adding 'chempy/water_residues.py' adding 'chempy/xyz.py' adding 'chempy/bmin/__init__.py' adding 'chempy/bmin/commands.py' adding 'chempy/bmin/realtime.py' adding 'chempy/bmin/state.py' adding 'chempy/bmin/util.py' adding 'chempy/champ/__init__.py' adding 'chempy/champ/_champ.cpython-313-x86_64-linux-gnu.so' adding 'chempy/champ/amber99.py' adding 'chempy/champ/assign.py' adding 'chempy/champ/formal_charges.py' adding 'chempy/fast/__init__.py' adding 'chempy/fragments/__init__.py' adding 'chempy/mmtf/__init__.py' adding 'chempy/mmtf/io.py' adding 'chempy/tinker/__init__.py' adding 'chempy/tinker/amber.py' adding 'chempy/tinker/keyword.py' adding 'chempy/tinker/realtime.py' adding 'chempy/tinker/state.py' adding 'pmg_qt/TextEditor.py' adding 'pmg_qt/__init__.py' adding 'pmg_qt/advanced_settings_gui.py' adding 'pmg_qt/builder.py' adding 'pmg_qt/file_dialogs.py' adding 'pmg_qt/keymapping.py' adding 'pmg_qt/mimic_pmg_tk.py' adding 'pmg_qt/mimic_tk.py' adding 'pmg_qt/properties_dialog.py' adding 'pmg_qt/pymol_gl_widget.py' adding 'pmg_qt/pymol_qt_gui.py' adding 'pmg_qt/scene_bin_gui.py' adding 'pmg_qt/shortcut_menu_gui.py' adding 'pmg_qt/volume.py' adding 'pmg_qt/forms/__init__.py' adding 'pmg_qt/forms/askpartial.ui' adding 'pmg_qt/forms/change_confirm.ui' adding 'pmg_qt/forms/colors.ui' adding 'pmg_qt/forms/create_shortcut.ui' adding 'pmg_qt/forms/fetch.ui' adding 'pmg_qt/forms/help_shortcut.ui' adding 'pmg_qt/forms/load_aln.ui' adding 'pmg_qt/forms/load_mae.ui' adding 'pmg_qt/forms/load_map.ui' adding 'pmg_qt/forms/load_mtz.ui' adding 'pmg_qt/forms/load_traj.ui' adding 'pmg_qt/forms/movieexport.ui' adding 'pmg_qt/forms/pluginitem.ui' adding 'pmg_qt/forms/pluginmanager.ui' adding 'pmg_qt/forms/png.ui' adding 'pmg_qt/forms/props.ui' adding 'pmg_qt/forms/render.ui' adding 'pmg_qt/forms/save_molecule.ui' adding 'pmg_qt/forms/save_object.ui' adding 'pmg_qt/forms/shortcut_menu.ui' adding 'pmg_qt/syntax/__init__.py' adding 'pmg_qt/syntax/pml.py' adding 'pmg_qt/syntax/pmlparser.py' adding 'pmg_qt/syntax/python.py' adding 'pmg_tk/ColorEditor.py' adding 'pmg_tk/Demo.py' adding 'pmg_tk/PMGApp.py' adding 'pmg_tk/PyMOLMapLoad.py' adding 'pmg_tk/SetEditor.py' adding 'pmg_tk/Setting.py' adding 'pmg_tk/TextEditor.py' adding 'pmg_tk/__init__.py' adding 'pmg_tk/volume.py' adding 'pmg_tk/skins/__init__.py' adding 'pmg_tk/skins/demo/__init__.py' adding 'pmg_tk/skins/normal/ModalWindow.py' adding 'pmg_tk/skins/normal/__init__.py' adding 'pmg_tk/skins/normal/builder.py' adding 'pmg_tk/startup/__init__.py' adding 'pymol/__init__.py' adding 'pymol/__main__.py' adding 'pymol/_cmd.cpython-313-x86_64-linux-gnu.so' adding 'pymol/_gui.py' adding 'pymol/api.py' adding 'pymol/callback.py' adding 'pymol/cgo.py' adding 'pymol/cgobuilder.py' adding 'pymol/checking.py' adding 'pymol/cmd.py' adding 'pymol/colorprinting.py' adding 'pymol/colorramping.py' adding 'pymol/commanding.py' adding 'pymol/completing.py' adding 'pymol/computing.py' adding 'pymol/constants.py' adding 'pymol/constants_palette.py' adding 'pymol/controlling.py' adding 'pymol/creating.py' adding 'pymol/diagnosing.py' adding 'pymol/editing.py' adding 'pymol/editor.py' adding 'pymol/experimenting.py' adding 'pymol/exporting.py' adding 'pymol/externing.py' adding 'pymol/feedingback.py' adding 'pymol/fitting.py' adding 'pymol/gui.py' adding 'pymol/headering.py' adding 'pymol/helping.py' adding 'pymol/importing.py' adding 'pymol/internal.py' adding 'pymol/invocation.py' adding 'pymol/keyboard.py' adding 'pymol/keywords.py' adding 'pymol/lazyio.py' adding 'pymol/locking.py' adding 'pymol/menu.py' adding 'pymol/monitoring.py' adding 'pymol/morphing.py' adding 'pymol/movie.py' adding 'pymol/moving.py' adding 'pymol/mpeg_encode.py' adding 'pymol/parser.py' adding 'pymol/parsing.py' adding 'pymol/povray.py' adding 'pymol/preset.py' adding 'pymol/pymolhttpd.py' adding 'pymol/querying.py' adding 'pymol/rpc.py' adding 'pymol/save_shortcut.py' adding 'pymol/selecting.py' adding 'pymol/selector.py' adding 'pymol/seqalign.py' adding 'pymol/setting.py' adding 'pymol/shortcut.py' adding 'pymol/shortcut_dict.py' adding 'pymol/shortcut_manager.py' adding 'pymol/util.py' adding 'pymol/vfont.py' adding 'pymol/viewing.py' adding 'pymol/wizarding.py' adding 'pymol/xray.py' adding 'pymol/xwin.py' adding 'pymol/Qt/__init__.py' adding 'pymol/Qt/utils.py' adding 'pymol/plugins/__init__.py' adding 'pymol/plugins/installation.py' adding 'pymol/plugins/legacysupport.py' adding 'pymol/plugins/managergui.py' adding 'pymol/plugins/managergui_qt.py' adding 'pymol/plugins/repository.py' adding 'pymol/pymol_path/LICENSE' adding 'pymol/pymol_path/data/chem_comp_bond-top100.cif' adding 'pymol/pymol_path/data/setting_help.csv' adding 'pymol/pymol_path/data/chempy/water.pdb' adding 'pymol/pymol_path/data/chempy/fragments/ace.pkl' adding 'pymol/pymol_path/data/chempy/fragments/acetylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/benzene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/butane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ct_val.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyanide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ethylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formamide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/formic.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/indane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/methane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/methanol.pkl' adding 'pymol/pymol_path/data/chempy/fragments/napthylene.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nhh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nitro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nme.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ala.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_arg.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_argn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_asph.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_cys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gln.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_glu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_gly.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hid.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hie.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_hip.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_his.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ile.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_leu.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_lys.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_met.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/nt_val.pkl' adding 'pymol/pymol_path/data/chempy/fragments/peptide.pkl' adding 'pymol/pymol_path/data/chempy/fragments/phe.pkl' adding 'pymol/pymol_path/data/chempy/fragments/phosphite.pkl' adding 'pymol/pymol_path/data/chempy/fragments/pro.pkl' adding 'pymol/pymol_path/data/chempy/fragments/realtime.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ser.pkl' adding 'pymol/pymol_path/data/chempy/fragments/sulfone.pkl' adding 'pymol/pymol_path/data/chempy/fragments/thr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl' adding 'pymol/pymol_path/data/chempy/fragments/trp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl' adding 'pymol/pymol_path/data/chempy/fragments/tyr.pkl' adding 'pymol/pymol_path/data/chempy/fragments/utp.pkl' adding 'pymol/pymol_path/data/chempy/fragments/utpA.pkl' adding 'pymol/pymol_path/data/chempy/fragments/val.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/generate1.py' adding 'pymol/pymol_path/data/chempy/sidechains/generate2.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl' adding 'pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py' adding 'pymol/pymol_path/data/chempy/sidechains/sc_library.pkl' adding 'pymol/pymol_path/data/chempy/tinker/Makefile.delsci' adding 'pymol/pymol_path/data/chempy/tinker/chempy.prm' adding 'pymol/pymol_path/data/chempy/tinker/make99_simple.py' adding 'pymol/pymol_path/data/chempy/tinker/make_simple.py' adding 'pymol/pymol_path/data/chempy/tinker/parm94.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm96.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99_simple.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm99_wld.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm_simple.dat' adding 'pymol/pymol_path/data/chempy/tinker/parm_simple.inp' adding 'pymol/pymol_path/data/demo/1hpv.r3d' adding 'pymol/pymol_path/data/demo/1tii.pdb' adding 'pymol/pymol_path/data/demo/cgo03.py' adding 'pymol/pymol_path/data/demo/il2.pdb' adding 'pymol/pymol_path/data/demo/pept.pdb' adding 'pymol/pymol_path/data/demo/pept.pkl' adding 'pymol/pymol_path/data/openvr/actions.json' adding 'pymol/pymol_path/data/openvr/bindings_vive_controller.json' adding 'pymol/pymol_path/data/openvr/hints_vive_controller.png' adding 'pymol/pymol_path/data/openvr/hints_vive_controller.svg' adding 'pymol/pymol_path/data/openvr/menu_splash.png' adding 'pymol/pymol_path/data/openvr/menu_splash.svg' adding 'pymol/pymol_path/data/pmg_qt/icons/refresh.svg' adding 'pymol/pymol_path/data/pmg_qt/styles/pymol.sty' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif' adding 'pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm' adding 'pymol/pymol_path/data/pymol/cmyk.png' adding 'pymol/pymol_path/data/pymol/hsv.ppm' adding 'pymol/pymol_path/data/pymol/splash.png' adding 'pymol/pymol_path/data/pymol/icons/icon2.svg' adding 'pymol/pymol_path/data/pymol/matrices/BLOSUM62' adding 'pymol/pymol_path/data/shaders/anaglyph_header.fs' adding 'pymol/pymol_path/data/shaders/bezier.fs' adding 'pymol/pymol_path/data/shaders/bezier.tsc' adding 'pymol/pymol_path/data/shaders/bezier.tse' adding 'pymol/pymol_path/data/shaders/bezier.vs' adding 'pymol/pymol_path/data/shaders/bg.fs' adding 'pymol/pymol_path/data/shaders/bg.vs' adding 'pymol/pymol_path/data/shaders/call_compute_color_for_light.fs' adding 'pymol/pymol_path/data/shaders/compute_color_for_light.fs' adding 'pymol/pymol_path/data/shaders/compute_fog_color.fs' adding 'pymol/pymol_path/data/shaders/connector.fs' adding 'pymol/pymol_path/data/shaders/connector.gs' adding 'pymol/pymol_path/data/shaders/connector.shared' adding 'pymol/pymol_path/data/shaders/connector.vs' adding 'pymol/pymol_path/data/shaders/copy.fs' adding 'pymol/pymol_path/data/shaders/copy.vs' adding 'pymol/pymol_path/data/shaders/cylinder.fs' adding 'pymol/pymol_path/data/shaders/cylinder.vs' adding 'pymol/pymol_path/data/shaders/default.fs' adding 'pymol/pymol_path/data/shaders/default.vs' adding 'pymol/pymol_path/data/shaders/indicator.fs' adding 'pymol/pymol_path/data/shaders/indicator.vs' adding 'pymol/pymol_path/data/shaders/label.fs' adding 'pymol/pymol_path/data/shaders/label.vs' adding 'pymol/pymol_path/data/shaders/line.fs' adding 'pymol/pymol_path/data/shaders/line.vs' adding 'pymol/pymol_path/data/shaders/oit.fs' adding 'pymol/pymol_path/data/shaders/oit.vs' adding 'pymol/pymol_path/data/shaders/ramp.fs' adding 'pymol/pymol_path/data/shaders/ramp.vs' adding 'pymol/pymol_path/data/shaders/screen.fs' adding 'pymol/pymol_path/data/shaders/screen.vs' adding 'pymol/pymol_path/data/shaders/sphere.fs' adding 'pymol/pymol_path/data/shaders/sphere.vs' adding 'pymol/pymol_path/data/shaders/surface.fs' adding 'pymol/pymol_path/data/shaders/surface.vs' adding 'pymol/pymol_path/data/shaders/trilines.fs' adding 'pymol/pymol_path/data/shaders/trilines.vs' adding 'pymol/pymol_path/data/shaders/volume.fs' adding 'pymol/pymol_path/data/shaders/volume.vs' adding 'pymol/pymol_path/data/shaders/vrcontroller.fs' adding 'pymol/pymol_path/data/shaders/vrcontroller.vs' adding 'pymol/pymol_path/data/shaders/webgl_header.fs' adding 'pymol/pymol_path/data/shaders/webgl_header.vs' adding 'pymol/pymol_path/data/startup/README.txt' adding 'pymol/pymol_path/data/startup/apbs_gui/__init__.py' adding 'pymol/pymol_path/data/startup/apbs_gui/apbs.ui' adding 'pymol/pymol_path/data/startup/apbs_gui/creating.py' adding 'pymol/pymol_path/data/startup/apbs_gui/electrostatics.py' adding 'pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py' adding 'pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py' adding 'pymol/pymol_path/data/startup/lightingsettings_gui/main.py' adding 'pymol/pymol_path/data/test/double.png' adding 'pymol/pymol_path/data/test/single-right.png' adding 'pymol/pymol_path/data/test/single.png' adding 'pymol/pymol_path/data/tut/1hpv.pdb' adding 'pymol/pymol_path/examples/chempy/generate_amber.py' adding 'pymol/pymol_path/examples/chempy/generate_mmff.py' adding 'pymol/pymol_path/examples/cookbook/area_diff.pml' adding 'pymol/pymol_path/examples/cookbook/build_peptide.py' adding 'pymol/pymol_path/examples/cookbook/contact.pml' adding 'pymol/pymol_path/examples/cookbook/dali.py' adding 'pymol/pymol_path/examples/cookbook/density.pml' adding 'pymol/pymol_path/examples/cookbook/groel_es.pml' adding 'pymol/pymol_path/examples/cookbook/multiclip_ray.pml' adding 'pymol/pymol_path/examples/cookbook/packing.pml' adding 'pymol/pymol_path/examples/cookbook/packsurf.pml' adding 'pymol/pymol_path/examples/cookbook/ref_frame.pml' adding 'pymol/pymol_path/examples/cookbook/ribosome.pml' adding 'pymol/pymol_path/examples/cookbook/scenes2movie.pml' adding 'pymol/pymol_path/examples/cookbook/seq_match_sele.pml' adding 'pymol/pymol_path/examples/cookbook/ss_xfer.pml' adding 'pymol/pymol_path/examples/cookbook/symsph.py' adding 'pymol/pymol_path/examples/devel/brick01.py' adding 'pymol/pymol_path/examples/devel/cam2crd.pym' adding 'pymol/pymol_path/examples/devel/cgo01.py' adding 'pymol/pymol_path/examples/devel/cgo02.py' adding 'pymol/pymol_path/examples/devel/cgo03.py' adding 'pymol/pymol_path/examples/devel/cgo04.py' adding 'pymol/pymol_path/examples/devel/cgo05.py' adding 'pymol/pymol_path/examples/devel/cgo06.py' adding 'pymol/pymol_path/examples/devel/cgo07.py' adding 'pymol/pymol_path/examples/devel/cgo08.py' adding 'pymol/pymol_path/examples/devel/cgo_3Dtext01.py' adding 'pymol/pymol_path/examples/devel/cgo_axes.py' adding 'pymol/pymol_path/examples/devel/cgo_label_hack.py' adding 'pymol/pymol_path/examples/devel/cgo_plane.py' adding 'pymol/pymol_path/examples/devel/chempy_model01.py' adding 'pymol/pymol_path/examples/devel/chempy_model02.py' adding 'pymol/pymol_path/examples/devel/chempy_model03.py' adding 'pymol/pymol_path/examples/devel/click_ordered_list.py' adding 'pymol/pymol_path/examples/devel/count_molecules.py' adding 'pymol/pymol_path/examples/devel/demo.sdf' adding 'pymol/pymol_path/examples/devel/extend_demo01.py' adding 'pymol/pymol_path/examples/devel/gl01.py' adding 'pymol/pymol_path/examples/devel/gl02.py' adding 'pymol/pymol_path/examples/devel/gl03.py' adding 'pymol/pymol_path/examples/devel/hole_vmd_tri.pym' adding 'pymol/pymol_path/examples/devel/importing.py' adding 'pymol/pymol_path/examples/devel/link_demo.py' adding 'pymol/pymol_path/examples/devel/membrane.py' adding 'pymol/pymol_path/examples/devel/mutate01.pml' adding 'pymol/pymol_path/examples/devel/mutate02.py' adding 'pymol/pymol_path/examples/devel/my_ext_gui.py' adding 'pymol/pymol_path/examples/devel/particle01.py' adding 'pymol/pymol_path/examples/devel/particle02.py' adding 'pymol/pymol_path/examples/devel/pick_wiz.py' adding 'pymol/pymol_path/examples/devel/povray01.py' adding 'pymol/pymol_path/examples/devel/scenes_to_movie01.pml' adding 'pymol/pymol_path/examples/devel/sd_annotate.pml' adding 'pymol/pymol_path/examples/devel/sele_wiz.py' adding 'pymol/pymol_path/examples/devel/start_pymol.py' adding 'pymol/pymol_path/examples/devel/syncmol.py' adding 'pymol/pymol_path/examples/devel/tkwindow.py' adding 'pymol/pymol_path/examples/devel/webgui01.py' adding 'pymol/pymol_path/examples/devel/webgui02.py' adding 'pymol/pymol_path/examples/devel/xmlrpc01.py' adding 'pymol/pymol_path/examples/devel/xmlrpc02.py' adding 'pymol/pymol_path/examples/launching/README' adding 'pymol/pymol_path/examples/launching/launch_demo.py' adding 'pymol/pymol_path/examples/launching/launch_viewer1.py' adding 'pymol/pymol_path/examples/launching/launch_viewer2.py' adding 'pymol/pymol_path/test/dat/1tii.pdb' adding 'pymol/pymol_path/test/dat/3al1.pdb' adding 'pymol/pymol_path/test/dat/3al1.r3d' adding 'pymol/pymol_path/test/dat/embed01.p1m' adding 'pymol/pymol_path/test/dat/embed02.p1m' adding 'pymol/pymol_path/test/dat/embed03.p1m' adding 'pymol/pymol_path/test/dat/embed04.p1m' adding 'pymol/pymol_path/test/dat/embed05.p1m' adding 'pymol/pymol_path/test/dat/embed06.p1m' adding 'pymol/pymol_path/test/dat/helix_amber.pdb' adding 'pymol/pymol_path/test/dat/il2.pdb' adding 'pymol/pymol_path/test/dat/ligs3d.sdf' adding 'pymol/pymol_path/test/dat/names.pdb' adding 'pymol/pymol_path/test/dat/odd01.pdb' adding 'pymol/pymol_path/test/dat/odd02.pdb' adding 'pymol/pymol_path/test/dat/pept.pdb' adding 'pymol/pymol_path/test/dat/pept.pkl' adding 'pymol/pymol_path/test/dat/pept.r3d' adding 'pymol/pymol_path/test/dat/small01.mol' adding 'pymol/pymol_path/test/dat/small02.pdb' adding 'pymol/pymol_path/test/dat/small03.mol2' adding 'pymol/pymol_path/test/dat/tiny.pdb' adding 'pymol/pymol_path/test/dat/water.pdb' adding 'pymol/stereochemistry/__init__.py' adding 'pymol/wizard/__init__.py' adding 'pymol/wizard/annotation.py' adding 'pymol/wizard/appearance.py' adding 'pymol/wizard/benchmark.py' adding 'pymol/wizard/box.py' adding 'pymol/wizard/charge.py' adding 'pymol/wizard/cleanup.py' adding 'pymol/wizard/command.py' adding 'pymol/wizard/demo.py' adding 'pymol/wizard/density.py' adding 'pymol/wizard/distance.py' adding 'pymol/wizard/dragging.py' adding 'pymol/wizard/filter.py' adding 'pymol/wizard/label.py' adding 'pymol/wizard/measurement.py' adding 'pymol/wizard/message.py' adding 'pymol/wizard/mutagenesis.py' adding 'pymol/wizard/nucmutagenesis.py' adding 'pymol/wizard/openvr.py' adding 'pymol/wizard/pair_fit.py' adding 'pymol/wizard/pseudoatom.py' adding 'pymol/wizard/renaming.py' adding 'pymol/wizard/sculpting.py' adding 'pymol/wizard/security.py' adding 'pymol/wizard/stereodemo.py' adding 'pymol/wizard/toggle.py' adding 'pymol-3.1.0.data/scripts/pymol' adding 'pymol-3.1.0.dist-info/licenses/AUTHORS' adding 'pymol-3.1.0.dist-info/licenses/LICENSE' 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/METADATA' adding 'pymol-3.1.0.dist-info/WHEEL' adding 'pymol-3.1.0.dist-info/entry_points.txt' adding 'pymol-3.1.0.dist-info/top_level.txt' adding 'pymol-3.1.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: pymol Building wheel for pymol (pyproject.toml): started Running command Building wheel for pymol (pyproject.toml) Building wheel for pymol (pyproject.toml): finished with status 'done' Created wheel for pymol: filename=pymol-3.1.0-cp313-cp313-linux_x86_64.whl size=44538573 sha256=5c7ef5a34ec4a8669e529a3028ab33d3234e77be3b3390bdde7f8e91e1240d9f 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.Gca5cd + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 ++ xargs basename --multiple ++ ls /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/pyproject-wheeldir/pymol-3.1.0-cp313-cp313-linux_x86_64.whl ++ 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 25.1.1 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_x86_64.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-3.1.0-7.fc43.x86_64-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-3.1.0-7.fc43.x86_64-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-3.1.0-7.fc43.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_FILES_ESCAPE=4.19 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-7.fc43.x86_64-pyproject-files --output-modules /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-7.fc43.x86_64-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-3.1.0-7.fc43.x86_64-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 "$@"' + ln -sfr /usr/lib64/python3.13/site-packages/pymol/pymol_path/data /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/pymol/data + 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 -j2 --strict-build-id -m -i --build-id-seed 3.1.0-7.fc43 --unique-debug-suffix -3.1.0-7.fc43.x86_64 --unique-debug-src-base pymol-3.1.0-7.fc43.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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-3.1.0-7.fc43.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/bin/pymol from /bin/sh to #!/usr/bin/sh *** WARNING: ./usr/src/debug/pymol-3.1.0-7.fc43.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-7.fc43.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-7.fc43.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-7.fc43.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 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 -j2 /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__/realtime.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__/util.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__/__init__.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/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/fast/__pycache__/__init__.cpython-313.pyc: rewriting with 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/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/mmtf/__pycache__/io.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/tinker/__pycache__/keyword.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/tinker/__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/tinker/__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/__pycache__/arc.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/chempy/__pycache__/bond_amber.cpython-313.pyc: rewriting with normalized 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/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/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/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 191 directories and 2222 files, processed 465 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.PzeMB5 + 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pymol-open-source-3.1.0 + PATH=/builddir/build/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-3.1.0-7.fc43.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.IWXEDp + 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 = 3.1.0-7.fc43 application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 3.1.0-7.fc43 pymol(x86-64) = 3.1.0-7.fc43 python-pymol = 3.1.0-7.fc43 python3-pymol = 3.1.0-7.fc43 python3.13-pymol = 3.1.0-7.fc43 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 libGL.so.1()(64bit) libGLEW.so.2.2()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.35)(64bit) libm.so.6(GLIBC_2.38)(64bit) libnetcdf.so.19()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) python(abi) = 3.13 rtld(GNU_HASH) Obsoletes: pymol < 0:3.1.0-5 Processing files: pymol+tests-3.1.0-7.fc43.x86_64 Provides: pymol+tests = 3.1.0-7.fc43 pymol+tests(x86-64) = 3.1.0-7.fc43 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-3.1.0-7.fc43.x86_64 Provides: pymol-debugsource = 3.1.0-7.fc43 pymol-debugsource(x86-64) = 3.1.0-7.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-3.1.0-7.fc43.x86_64 Provides: debuginfo(build-id) = 6697e97f438f7d7fa6175fc4309e1c1a13633801 debuginfo(build-id) = 940ab19d6686abfac76c63e2d499971f38441669 pymol-debuginfo = 3.1.0-7.fc43 pymol-debuginfo(x86-64) = 3.1.0-7.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(x86-64) = 3.1.0-7.fc43 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT Wrote: /builddir/build/SRPMS/pymol-3.1.0-7.fc43.src.rpm Wrote: /builddir/build/RPMS/pymol+tests-3.1.0-7.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-3.1.0-7.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-3.1.0-7.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-3.1.0-7.fc43.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.kjOGLD + 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-3.1.0-7.fc43.src.rpm Finish: build phase for pymol-3.1.0-7.fc43.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1748989340.287934/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-3.1.0-7.fc43.src.rpm) Config(child) 9 minutes 13 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "7.fc43", "arch": "src" }, { "name": "pymol-debugsource", "epoch": null, "version": "3.1.0", "release": "7.fc43", "arch": "x86_64" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "7.fc43", "arch": "x86_64" }, { "name": "pymol+tests", "epoch": null, "version": "3.1.0", "release": "7.fc43", "arch": "x86_64" }, { "name": "pymol-debuginfo", "epoch": null, "version": "3.1.0", "release": "7.fc43", "arch": "x86_64" } ] } RPMResults finished