Warning: Permanently added '54.234.117.223' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10122498-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.6 PID: 15662 Logging PID: 15664 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 10122498, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '81d0e83362d223b1c4ef35e1d9ff817a6b3fcbea', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-pip/pymol', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'pymol', 'package_version': '3.1.0-14', 'project_dirname': 'python-pip', 'project_name': 'python-pip', 'project_owner': 'thrnciar', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/thrnciar/python-pip/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'thrnciar/python-pip--thrnciar', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'thrnciar', 'tags': [], 'task_id': '10122498-fedora-rawhide-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-pip/pymol /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-pip/pymol', '/var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol'... Running: git checkout 81d0e83362d223b1c4ef35e1d9ff817a6b3fcbea -- cmd: ['git', 'checkout', '81d0e83362d223b1c4ef35e1d9ff817a6b3fcbea', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol rc: 0 stdout: stderr: Note: switching to '81d0e83362d223b1c4ef35e1d9ff817a6b3fcbea'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 81d0e83 automatic import of pymol Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading pymol-open-source-3.1.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o pymol-open-source-3.1.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/thrnciar/python-pip/pymol/pymol-open-source-3.1.0.tar.gz/md5/459f483231e1d521824b0e74df5ba640/pymol-open-source-3.1.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 28.1M 100 28.1M 0 0 27.8M 0 0:00:01 0:00:01 --:--:-- 27.8M INFO: Reading stdout from command: md5sum pymol-open-source-3.1.0.tar.gz INFO: Downloading pymol.png INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o pymol.png --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/thrnciar/python-pip/pymol/pymol.png/md5/3bbd85dbd40f588f505ad988b6df2933/pymol.png % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 19466 100 19466 0 0 586k 0 --:--:-- --:--:-- --:--:-- 594k INFO: Reading stdout from command: md5sum pymol.png tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1770926021.807988 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-1sfby99c/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1770926021.807988 -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-1sfby99c/pymol/pymol.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1770926021.807988/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-2a426527-3c80-4a6c-8eb3-470174f4463e INFO: Checking that 0a0c439658dd7b75bf8f5a843f3a9ca0dca6343bdd3fd1676ba95b9bec4a9634 image matches host's architecture INFO: Copy content of container 0a0c439658dd7b75bf8f5a843f3a9ca0dca6343bdd3fd1676ba95b9bec4a9634 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1770926021.807988/root INFO: mounting 0a0c439658dd7b75bf8f5a843f3a9ca0dca6343bdd3fd1676ba95b9bec4a9634 with podman image mount INFO: image 0a0c439658dd7b75bf8f5a843f3a9ca0dca6343bdd3fd1676ba95b9bec4a9634 as /var/lib/containers/storage/overlay/ede174b9c190f9a3ee296a0c6e28ac5a6a3fffc4b918cdd69606e7fc6d1392f1/merged INFO: umounting image 0a0c439658dd7b75bf8f5a843f3a9ca0dca6343bdd3fd1676ba95b9bec4a9634 (/var/lib/containers/storage/overlay/ede174b9c190f9a3ee296a0c6e28ac5a6a3fffc4b918cdd69606e7fc6d1392f1/merged) with podman image umount INFO: Removing image mock-bootstrap-2a426527-3c80-4a6c-8eb3-470174f4463e 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_64-1770926021.807988/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-6.0.1-3.fc45.x86_64 rpm-sequoia-1.10.0-2.fc44.x86_64 dnf5-5.3.0.0-7.fc44.x86_64 dnf5-plugins-5.3.0.0-7.fc44.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 90.1 KiB/s | 1.5 KiB | 00m00s fedora 100% | 183.8 KiB/s | 23.0 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 0:5.3.9-3.fc44 fedora 8.5 MiB bzip2 x86_64 0:1.0.8-23.fc44 fedora 95.0 KiB coreutils x86_64 0:9.10-1.fc45 fedora 5.6 MiB cpio x86_64 0:2.15-9.fc44 fedora 1.1 MiB diffutils x86_64 0:3.12-5.fc44 fedora 1.6 MiB fedora-release-common noarch 0:45-0.1 fedora 20.5 KiB findutils x86_64 1:4.10.0-7.fc44 fedora 1.9 MiB gawk x86_64 0:5.3.2-3.fc44 fedora 1.8 MiB glibc-minimal-langpack x86_64 0:2.43.9000-1.fc45 fedora 0.0 B grep x86_64 0:3.12-3.fc44 fedora 1.0 MiB gzip x86_64 0:1.14-2.fc44 fedora 401.6 KiB info x86_64 0:7.2-7.fc44 fedora 357.9 KiB patch x86_64 0:2.8-4.fc44 fedora 226.6 KiB redhat-rpm-config noarch 0:343-19.fc44 fedora 183.6 KiB rpm-build x86_64 0:6.0.1-3.fc45 fedora 294.6 KiB sed x86_64 0:4.9-8.fc45 fedora 857.2 KiB shadow-utils x86_64 2:4.19.0-6.fc44 fedora 4.0 MiB tar x86_64 2:1.35-8.fc44 fedora 3.0 MiB unzip x86_64 0:6.0-69.fc44 fedora 445.8 KiB util-linux x86_64 0:2.41.3-12.fc44 fedora 3.5 MiB which x86_64 0:2.23-4.fc44 fedora 83.4 KiB xz x86_64 1:5.8.2-2.fc44 fedora 1.3 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.4-3.fc44 fedora 3.4 KiB add-determinism x86_64 0:0.7.2-4.fc45 fedora 2.2 MiB alternatives x86_64 0:1.33-5.fc44 fedora 62.1 KiB ansible-srpm-macros noarch 0:1-20.1.fc44 fedora 35.7 KiB audit-libs x86_64 0:4.1.3-1.fc44 fedora 390.5 KiB binutils x86_64 0:2.46-1.fc45 fedora 27.2 MiB build-reproducibility-srpm-macros noarch 0:0.7.2-4.fc45 fedora 1.2 KiB bzip2-libs x86_64 0:1.0.8-23.fc44 fedora 80.5 KiB ca-certificates noarch 0:2025.2.80_v9.0.304-5.fc44 fedora 2.7 MiB cmake-srpm-macros noarch 0:4.2.3-1.fc45 fedora 524.0 B coreutils-common x86_64 0:9.10-1.fc45 fedora 10.7 MiB crypto-policies noarch 0:20251128-3.git19878fe.fc44 fedora 132.6 KiB curl x86_64 0:8.18.0-4.fc45 fedora 480.0 KiB cyrus-sasl-lib x86_64 0:2.1.28-35.fc44 fedora 2.3 MiB debugedit x86_64 0:5.2-6.fc44 fedora 218.3 KiB dwz x86_64 0:0.16-3.fc44 fedora 290.9 KiB ed x86_64 0:1.22.4-2.fc44 fedora 149.1 KiB efi-srpm-macros noarch 0:6-6.fc44 fedora 40.2 KiB elfutils x86_64 0:0.194-3.fc44 fedora 2.9 MiB elfutils-debuginfod-client x86_64 0:0.194-3.fc44 fedora 83.7 KiB elfutils-default-yama-scope noarch 0:0.194-3.fc44 fedora 1.8 KiB elfutils-libelf x86_64 0:0.194-3.fc44 fedora 1.1 MiB elfutils-libs x86_64 0:0.194-3.fc44 fedora 715.3 KiB fedora-gpg-keys noarch 0:45-0.1 fedora 133.4 KiB fedora-release noarch 0:45-0.1 fedora 0.0 B fedora-release-identity-basic noarch 0:45-0.1 fedora 664.0 B fedora-repos noarch 0:45-0.1 fedora 4.9 KiB fedora-repos-rawhide noarch 0:45-0.1 fedora 2.2 KiB file x86_64 0:5.46-9.fc44 fedora 100.1 KiB file-libs x86_64 0:5.46-9.fc44 fedora 11.9 MiB filesystem x86_64 0:3.18-52.fc44 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-52.fc44 fedora 38.2 KiB fonts-srpm-macros noarch 1:5.0.0-2.fc44 fedora 55.8 KiB forge-srpm-macros noarch 0:0.4.0-4.fc44 fedora 38.9 KiB fpc-srpm-macros noarch 0:1.3-16.fc44 fedora 144.0 B gap-srpm-macros noarch 0:2-2.fc44 fedora 2.1 KiB gdb-minimal x86_64 0:17.1-2.fc44 fedora 14.3 MiB gdbm-libs x86_64 1:1.23-11.fc44 fedora 129.6 KiB ghc-srpm-macros noarch 0:1.10-1.fc44 fedora 792.0 B glibc x86_64 0:2.43.9000-1.fc45 fedora 7.0 MiB glibc-common x86_64 0:2.43.9000-1.fc45 fedora 1.0 MiB glibc-gconv-extra x86_64 0:2.43.9000-1.fc45 fedora 7.7 MiB gmp x86_64 1:6.3.0-5.fc44 fedora 815.2 KiB gnat-srpm-macros noarch 0:7-2.fc44 fedora 1.0 KiB gnulib-l10n noarch 0:20241231-2.fc44 fedora 655.0 KiB gnupg2 x86_64 0:2.4.9-5.fc44 fedora 6.5 MiB gnupg2-dirmngr x86_64 0:2.4.9-5.fc44 fedora 633.9 KiB gnupg2-gpg-agent x86_64 0:2.4.9-5.fc44 fedora 682.5 KiB gnupg2-gpgconf x86_64 0:2.4.9-5.fc44 fedora 249.7 KiB gnupg2-keyboxd x86_64 0:2.4.9-5.fc44 fedora 201.2 KiB gnupg2-verify x86_64 0:2.4.9-5.fc44 fedora 360.3 KiB gnutls x86_64 0:3.8.12-1.fc45 fedora 3.7 MiB go-srpm-macros noarch 0:3.8.0-2.fc44 fedora 61.9 KiB gpgverify noarch 0:2.2-4.fc44 fedora 8.7 KiB ima-evm-utils-libs x86_64 0:1.6.2-8.fc44 fedora 60.6 KiB jansson x86_64 0:2.14-4.fc44 fedora 88.9 KiB java-srpm-macros noarch 0:1-8.fc44 fedora 870.0 B json-c x86_64 0:0.18-8.fc44 fedora 82.6 KiB kernel-srpm-macros noarch 0:1.0-28.fc44 fedora 1.9 KiB keyutils-libs x86_64 0:1.6.3-7.fc44 fedora 54.2 KiB krb5-libs x86_64 0:1.21.3-12.fc44 fedora 2.4 MiB libacl x86_64 0:2.3.2-6.fc44 fedora 35.8 KiB libarchive x86_64 0:3.8.4-2.fc44 fedora 991.2 KiB libassuan x86_64 0:2.5.7-5.fc44 fedora 163.8 KiB libattr x86_64 0:2.5.2-8.fc44 fedora 24.3 KiB libblkid x86_64 0:2.41.3-12.fc44 fedora 274.3 KiB libbrotli x86_64 0:1.2.0-3.fc45 copr_base 865.0 KiB libcap x86_64 0:2.77-2.fc44 fedora 212.1 KiB libcap-ng x86_64 0:0.9-7.fc44 fedora 68.7 KiB libcbor x86_64 0:0.13.0-2.fc44 fedora 79.5 KiB libcom_err x86_64 0:1.47.3-4.fc44 fedora 63.0 KiB libcurl x86_64 0:8.18.0-4.fc45 fedora 1.0 MiB libeconf x86_64 0:0.7.9-3.fc44 fedora 64.8 KiB libevent x86_64 0:2.1.12-17.fc44 fedora 978.7 KiB libfdisk x86_64 0:2.41.3-12.fc44 fedora 388.3 KiB libffi x86_64 0:3.5.2-2.fc44 fedora 87.7 KiB libfido2 x86_64 0:1.16.0-5.fc44 fedora 246.4 KiB libfsverity x86_64 0:1.6-4.fc44 fedora 28.4 KiB libgcc x86_64 0:16.0.1-0.7.fc45 fedora 270.7 KiB libgcrypt x86_64 0:1.11.2-1.fc44 fedora 1.6 MiB libgomp x86_64 0:16.0.1-0.7.fc45 fedora 572.5 KiB libgpg-error x86_64 0:1.58-2.fc44 fedora 941.6 KiB libidn2 x86_64 0:2.3.8-3.fc44 fedora 556.4 KiB libksba x86_64 0:1.6.7-5.fc44 fedora 414.4 KiB liblastlog2 x86_64 0:2.41.3-12.fc44 fedora 37.6 KiB libmount x86_64 0:2.41.3-12.fc44 fedora 388.6 KiB libnghttp2 x86_64 0:1.68.0-3.fc44 fedora 166.1 KiB libnghttp3 x86_64 0:1.15.0-1.fc44 fedora 159.2 KiB libpkgconf x86_64 0:2.3.0-4.fc44 fedora 78.0 KiB libpsl x86_64 0:0.21.5-7.fc44 fedora 76.3 KiB libselinux x86_64 0:3.10-1.fc45 copr_base 201.0 KiB libselinux-utils x86_64 0:3.10-1.fc45 copr_base 305.7 KiB libsemanage x86_64 0:3.10-1.fc44 fedora 312.3 KiB libsepol x86_64 0:3.10-1.fc44 fedora 870.0 KiB libsmartcols x86_64 0:2.41.3-12.fc44 fedora 188.3 KiB libssh x86_64 0:0.12.0-1.fc45 fedora 719.1 KiB libssh-config noarch 0:0.12.0-1.fc45 fedora 277.0 B libstdc++ x86_64 0:16.0.1-0.7.fc45 fedora 2.9 MiB libtasn1 x86_64 0:4.20.0-3.fc44 fedora 180.2 KiB libtool-ltdl x86_64 0:2.5.4-10.fc44 fedora 70.0 KiB libunistring x86_64 0:1.1-11.fc44 fedora 1.7 MiB libusb1 x86_64 0:1.0.29-5.fc44 fedora 175.2 KiB libuuid x86_64 0:2.41.3-12.fc44 fedora 37.2 KiB libverto x86_64 0:0.3.2-12.fc44 fedora 25.3 KiB libxcrypt x86_64 0:4.5.2-3.fc44 fedora 293.2 KiB libxml2 x86_64 0:2.12.10-6.fc44 fedora 1.8 MiB libzstd x86_64 0:1.5.7-5.fc44 fedora 956.1 KiB linkdupes x86_64 0:0.7.2-4.fc45 fedora 789.3 KiB lua-srpm-macros noarch 0:1-17.fc44 fedora 1.3 KiB lua5.4-libs x86_64 0:5.5.0-1.fc45 fedora 281.7 KiB lz4-libs x86_64 0:1.10.0-4.fc44 fedora 157.3 KiB mpfr x86_64 0:4.2.2-3.fc44 fedora 849.1 KiB ncurses-base noarch 0:6.6-1.fc44 fedora 329.7 KiB ncurses-libs x86_64 0:6.6-1.fc44 fedora 968.9 KiB nettle x86_64 0:3.10.1-3.fc44 fedora 794.3 KiB ngtcp2 x86_64 0:1.19.0-2.fc44 fedora 330.2 KiB ngtcp2-crypto-ossl x86_64 0:1.19.0-2.fc44 fedora 51.6 KiB npth x86_64 0:1.8-4.fc44 fedora 49.5 KiB ocaml-srpm-macros noarch 0:11-3.fc44 fedora 1.9 KiB openblas-srpm-macros noarch 0:2-21.fc44 fedora 112.0 B openldap x86_64 0:2.6.10-7.fc44 fedora 667.5 KiB openssl-libs x86_64 1:3.5.5-1.fc44 fedora 9.2 MiB p11-kit x86_64 0:0.26.2-1.fc45 fedora 2.6 MiB p11-kit-trust x86_64 0:0.26.2-1.fc45 fedora 478.3 KiB package-notes-srpm-macros noarch 0:0.17-3.fc45 fedora 1.6 KiB pam-libs x86_64 0:1.7.2-1.fc44 fedora 130.5 KiB pcre2 x86_64 0:10.47-1.fc44.1 fedora 718.6 KiB pcre2-syntax noarch 0:10.47-1.fc44.1 fedora 281.9 KiB perl-srpm-macros noarch 0:1-61.fc44 fedora 861.0 B pkgconf x86_64 0:2.3.0-4.fc44 fedora 88.3 KiB pkgconf-m4 noarch 0:2.3.0-4.fc44 fedora 14.4 KiB pkgconf-pkg-config x86_64 0:2.3.0-4.fc44 fedora 989.0 B policycoreutils x86_64 0:3.10-1.fc45 copr_base 884.1 KiB popt x86_64 0:1.19-10.fc44 fedora 132.6 KiB publicsuffix-list-dafsa noarch 0:20260116-1.fc44 fedora 70.4 KiB pyproject-srpm-macros noarch 0:1.18.6-2.fc44 fedora 1.9 KiB python-srpm-macros noarch 0:3.14-10.fc44 fedora 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-2.fc44 fedora 500.0 B qt6-srpm-macros noarch 0:6.10.2-1.fc45 fedora 472.0 B readline x86_64 0:8.3-4.fc44 fedora 519.5 KiB rpm x86_64 0:6.0.1-3.fc45 fedora 3.1 MiB rpm-build-libs x86_64 0:6.0.1-3.fc45 fedora 276.3 KiB rpm-libs x86_64 0:6.0.1-3.fc45 fedora 961.2 KiB rpm-plugin-selinux x86_64 0:6.0.1-3.fc45 fedora 11.9 KiB rpm-sequoia x86_64 0:1.10.0-2.fc44 fedora 2.5 MiB rpm-sign-libs x86_64 0:6.0.1-3.fc45 fedora 39.6 KiB rust-srpm-macros noarch 0:28.4-3.fc44 fedora 5.5 KiB selinux-policy noarch 0:42.23-1.fc44 fedora 32.0 KiB selinux-policy-targeted noarch 0:42.23-1.fc44 fedora 18.5 MiB setup noarch 0:2.15.0-28.fc44 fedora 724.9 KiB sqlite-libs x86_64 0:3.51.2-1.fc44 fedora 1.6 MiB systemd-libs x86_64 0:259.1-1.fc45 fedora 2.4 MiB systemd-standalone-sysusers x86_64 0:259.1-1.fc45 fedora 305.7 KiB tpm2-tss x86_64 0:4.1.3-9.fc44 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0:0.4.2-2.fc44 fedora 8.3 KiB util-linux-core x86_64 0:2.41.3-12.fc44 fedora 1.5 MiB xxhash-libs x86_64 0:0.8.3-4.fc44 fedora 94.0 KiB xz-libs x86_64 1:5.8.2-2.fc44 fedora 217.7 KiB zig-srpm-macros noarch 0:1-8.fc44 fedora 1.3 KiB zip x86_64 0:3.0-45.fc44 fedora 698.0 KiB zlib-ng-compat x86_64 0:2.3.3-2.fc45 fedora 165.6 KiB zstd x86_64 0:1.5.7-5.fc44 fedora 502.4 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 184 packages Total size of inbound packages is 69 MiB. Need to download 0 B. After this operation, 223 MiB extra will be used (install 223 MiB, remove 0 B). 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B | 00m00s >>> Already downloaded [170/184] ngtcp2-0:1.19.0-2.fc44.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [171/184] ngtcp2-crypto-ossl-0:1.19.0-2 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [172/184] keyutils-libs-0:1.6.3-7.fc44. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [173/184] libcom_err-0:1.47.3-4.fc44.x8 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [174/184] libverto-0:0.3.2-12.fc44.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [175/184] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [176/184] libfido2-0:1.16.0-5.fc44.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [177/184] libssh-config-0:0.12.0-1.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [178/184] libcbor-0:0.13.0-2.fc44.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [179/184] selinux-policy-targeted-0:42. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [180/184] selinux-policy-0:42.23-1.fc44 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [181/184] rpm-plugin-selinux-0:6.0.1-3. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [182/184] policycoreutils-0:3.10-1.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [183/184] libselinux-utils-0:3.10-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [184/184] libbrotli-0:1.2.0-3.fc45.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [184/184] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-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. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. [ 1/186] Verify package files 100% | 669.0 B/s | 184.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-52.fc44.x86_64 >>> Finished %pretrans scriptlet: filesystem-0:3.18-52.fc44.x86_64 >>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1770926021.807988/root/var/cache/dnf/copr_base-599f2dc1e3e330e5/packages/libselinux-3.10-1.fc45.x86_64.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 334e731f61c664d2: NOKEY [ 2/186] Prepare transaction 100% | 3.3 KiB/s | 184.0 B | 00m00s [ 3/186] Installing libgcc-0:16.0.1-0. 100% | 266.0 MiB/s | 272.4 KiB | 00m00s [ 4/186] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/186] Installing publicsuffix-list- 100% | 0.0 B/s | 71.1 KiB | 00m00s [ 6/186] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 7/186] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 8/186] Installing fedora-gpg-keys-0: 100% | 44.5 MiB/s | 182.1 KiB | 00m00s [ 9/186] Installing fedora-repos-0:45- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/186] Installing fedora-release-com 100% | 24.2 MiB/s | 24.8 KiB | 00m00s [ 11/186] Installing fedora-release-0:4 100% | 20.2 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-28.fc44.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-28.fc44.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. >>> [ 12/186] Installing setup-0:2.15.0-28. 100% | 47.6 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/186] Installing filesystem-0:3.18- 100% | 2.7 MiB/s | 212.8 KiB | 00m00s [ 14/186] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 15/186] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB | 00m00s [ 16/186] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 17/186] Installing coreutils-common-0 100% | 356.2 MiB/s | 10.7 MiB | 00m00s [ 18/186] Installing ncurses-base-0:6.6 100% | 86.7 MiB/s | 355.3 KiB | 00m00s [ 19/186] Installing bash-0:5.3.9-3.fc4 100% | 273.6 MiB/s | 8.5 MiB | 00m00s [ 20/186] Installing glibc-common-0:2.4 100% | 60.6 MiB/s | 1.0 MiB | 00m00s [ 21/186] Installing glibc-gconv-extra- 100% | 287.3 MiB/s | 7.8 MiB | 00m00s [ 22/186] Installing glibc-0:2.43.9000- 100% | 183.3 MiB/s | 7.0 MiB | 00m00s [ 23/186] Installing ncurses-libs-0:6.6 100% | 238.1 MiB/s | 975.4 KiB | 00m00s [ 24/186] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 25/186] Installing zlib-ng-compat-0:2 100% | 162.6 MiB/s | 166.5 KiB | 00m00s [ 26/186] Installing bzip2-libs-0:1.0.8 100% | 79.7 MiB/s | 81.6 KiB | 00m00s [ 27/186] Installing libgpg-error-0:1.5 100% | 61.7 MiB/s | 947.5 KiB | 00m00s [ 28/186] Installing libstdc++-0:16.0.1 100% | 365.3 MiB/s | 2.9 MiB | 00m00s [ 29/186] Installing libassuan-0:2.5.7- 100% | 161.8 MiB/s | 165.7 KiB | 00m00s [ 30/186] Installing libgcrypt-0:1.11.2 100% | 394.0 MiB/s | 1.6 MiB | 00m00s [ 31/186] Installing readline-0:8.3-4.f 100% | 254.7 MiB/s | 521.6 KiB | 00m00s [ 32/186] Installing gmp-1:6.3.0-5.fc44 100% | 399.2 MiB/s | 817.5 KiB | 00m00s [ 33/186] Installing xz-libs-1:5.8.2-2. 100% | 213.7 MiB/s | 218.8 KiB | 00m00s [ 34/186] Installing libuuid-0:2.41.3-1 100% | 37.3 MiB/s | 38.2 KiB | 00m00s [ 35/186] Installing popt-0:1.19-10.fc4 100% | 68.0 MiB/s | 139.3 KiB | 00m00s [ 36/186] Installing systemd-libs-0:259 100% | 348.9 MiB/s | 2.4 MiB | 00m00s [ 37/186] Installing libzstd-0:1.5.7-5. 100% | 311.6 MiB/s | 957.4 KiB | 00m00s [ 38/186] Installing elfutils-libelf-0: 100% | 376.3 MiB/s | 1.1 MiB | 00m00s [ 39/186] Installing npth-0:1.8-4.fc44. 100% | 0.0 B/s | 50.6 KiB | 00m00s [ 40/186] Installing libblkid-0:2.41.3- 100% | 269.0 MiB/s | 275.4 KiB | 00m00s [ 41/186] Installing libxcrypt-0:4.5.2- 100% | 289.0 MiB/s | 295.9 KiB | 00m00s [ 42/186] Installing sqlite-libs-0:3.51 100% | 318.1 MiB/s | 1.6 MiB | 00m00s [ 43/186] Installing libsepol-0:3.10-1. 100% | 283.5 MiB/s | 871.0 KiB | 00m00s [ 44/186] Installing gnupg2-gpgconf-0:2 100% | 18.9 MiB/s | 251.8 KiB | 00m00s [ 45/186] Installing libattr-0:2.5.2-8. 100% | 0.0 B/s | 25.2 KiB | 00m00s [ 46/186] Installing libacl-0:2.3.2-6.f 100% | 0.0 B/s | 36.6 KiB | 00m00s [ 47/186] Installing pcre2-0:10.47-1.fc 100% | 351.6 MiB/s | 720.0 KiB | 00m00s [ 48/186] Installing libselinux-0:3.10- 100% | 197.5 MiB/s | 202.3 KiB | 00m00s [ 49/186] Installing grep-0:3.12-3.fc44 100% | 62.7 MiB/s | 1.0 MiB | 00m00s [ 50/186] Installing sed-0:4.9-8.fc45.x 100% | 56.3 MiB/s | 865.4 KiB | 00m00s [ 51/186] Installing findutils-1:4.10.0 100% | 103.9 MiB/s | 1.9 MiB | 00m00s [ 52/186] Installing libtasn1-0:4.20.0- 100% | 177.7 MiB/s | 182.0 KiB | 00m00s [ 53/186] Installing libunistring-0:1.1 100% | 346.9 MiB/s | 1.7 MiB | 00m00s [ 54/186] Installing libidn2-0:2.3.8-3. 100% | 61.0 MiB/s | 562.6 KiB | 00m00s [ 55/186] Installing crypto-policies-0: 100% | 30.8 MiB/s | 157.7 KiB | 00m00s [ 56/186] Installing xz-1:5.8.2-2.fc44. 100% | 72.1 MiB/s | 1.4 MiB | 00m00s [ 57/186] Installing libmount-0:2.41.3- 100% | 190.3 MiB/s | 389.7 KiB | 00m00s [ 58/186] Installing gnupg2-verify-0:2. 100% | 27.2 MiB/s | 361.7 KiB | 00m00s [ 59/186] Installing dwz-0:0.16-3.fc44. 100% | 22.0 MiB/s | 292.3 KiB | 00m00s [ 60/186] Installing mpfr-0:4.2.2-3.fc4 100% | 276.9 MiB/s | 850.8 KiB | 00m00s [ 61/186] Installing gawk-0:5.3.2-3.fc4 100% | 101.9 MiB/s | 1.8 MiB | 00m00s [ 62/186] Installing libksba-0:1.6.7-5. 100% | 203.6 MiB/s | 416.9 KiB | 00m00s [ 63/186] Installing unzip-0:6.0-69.fc4 100% | 33.8 MiB/s | 449.3 KiB | 00m00s [ 64/186] Installing file-libs-0:5.46-9 100% | 624.3 MiB/s | 11.9 MiB | 00m00s [ 65/186] Installing file-0:5.46-9.fc44 100% | 7.6 MiB/s | 101.6 KiB | 00m00s [ 66/186] Installing diffutils-0:3.12-5 100% | 92.5 MiB/s | 1.6 MiB | 00m00s [ 67/186] Installing libeconf-0:0.7.9-3 100% | 64.9 MiB/s | 66.4 KiB | 00m00s [ 68/186] Installing libcap-ng-0:0.9-7. 100% | 68.9 MiB/s | 70.5 KiB | 00m00s [ 69/186] Installing audit-libs-0:4.1.3 100% | 191.9 MiB/s | 393.1 KiB | 00m00s [ 70/186] Installing pam-libs-0:1.7.2-1 100% | 129.8 MiB/s | 132.9 KiB | 00m00s [ 71/186] Installing libcap-0:2.77-2.fc 100% | 16.3 MiB/s | 217.2 KiB | 00m00s [ 72/186] Installing libsemanage-0:3.10 100% | 306.7 MiB/s | 314.1 KiB | 00m00s [ 73/186] Installing libsmartcols-0:2.4 100% | 184.9 MiB/s | 189.3 KiB | 00m00s [ 74/186] Installing lua5.4-libs-0:5.5. 100% | 276.3 MiB/s | 283.0 KiB | 00m00s [ 75/186] Installing json-c-0:0.18-8.fc 100% | 81.9 MiB/s | 83.9 KiB | 00m00s [ 76/186] Installing libffi-0:3.5.2-2.f 100% | 87.0 MiB/s | 89.1 KiB | 00m00s [ 77/186] Installing p11-kit-0:0.26.2-1 100% | 123.6 MiB/s | 2.6 MiB | 00m00s [ 78/186] Installing alternatives-0:1.3 100% | 5.2 MiB/s | 63.6 KiB | 00m00s [ 79/186] Installing p11-kit-trust-0:0. 100% | 23.4 MiB/s | 480.0 KiB | 00m00s [ 80/186] Installing ngtcp2-0:1.19.0-2. 100% | 162.0 MiB/s | 331.7 KiB | 00m00s [ 81/186] Installing openssl-libs-1:3.5 100% | 367.5 MiB/s | 9.2 MiB | 00m00s [ 82/186] Installing coreutils-0:9.10-1 100% | 167.4 MiB/s | 5.7 MiB | 00m00s [ 83/186] Installing ca-certificates-0: 100% | 2.0 MiB/s | 2.5 MiB | 00m01s [ 84/186] Installing gzip-0:1.14-2.fc44 100% | 26.5 MiB/s | 407.1 KiB | 00m00s [ 85/186] Installing rpm-sequoia-0:1.10 100% | 352.3 MiB/s | 2.5 MiB | 00m00s [ 86/186] Installing libfsverity-0:1.6- 100% | 28.7 MiB/s | 29.4 KiB | 00m00s [ 87/186] Installing libevent-0:2.1.12- 100% | 319.8 MiB/s | 982.4 KiB | 00m00s [ 88/186] Installing ngtcp2-crypto-ossl 100% | 51.2 MiB/s | 52.5 KiB | 00m00s [ 89/186] Installing util-linux-core-0: 100% | 82.4 MiB/s | 1.5 MiB | 00m00s [ 90/186] Installing zip-0:3.0-45.fc44. 100% | 49.0 MiB/s | 701.9 KiB | 00m00s [ 91/186] Installing gnupg2-keyboxd-0:2 100% | 33.0 MiB/s | 202.5 KiB | 00m00s [ 92/186] Installing libpsl-0:0.21.5-7. 100% | 75.6 MiB/s | 77.4 KiB | 00m00s [ 93/186] Installing tar-2:1.35-8.fc44. 100% | 135.4 MiB/s | 3.0 MiB | 00m00s [ 94/186] Installing linkdupes-0:0.7.2- 100% | 51.5 MiB/s | 790.7 KiB | 00m00s [ 95/186] Installing libselinux-utils-0 100% | 22.3 MiB/s | 319.7 KiB | 00m00s [ 96/186] Installing liblastlog2-0:2.41 100% | 7.8 MiB/s | 39.8 KiB | 00m00s [ 97/186] Installing systemd-standalone 100% | 21.4 MiB/s | 306.2 KiB | 00m00s [ 98/186] Installing rpm-libs-0:6.0.1-3 100% | 313.4 MiB/s | 962.7 KiB | 00m00s [ 99/186] Installing libfdisk-0:2.41.3- 100% | 126.8 MiB/s | 389.4 KiB | 00m00s [100/186] Installing util-linux-0:2.41. 100% | 102.4 MiB/s | 3.6 MiB | 00m00s [101/186] Installing policycoreutils-0: 100% | 35.6 MiB/s | 912.5 KiB | 00m00s [102/186] Installing selinux-policy-0:4 100% | 1.8 MiB/s | 33.6 KiB | 00m00s [103/186] Installing selinux-policy-tar 100% | 185.1 MiB/s | 14.8 MiB | 00m00s [104/186] Installing zstd-0:1.5.7-5.fc4 100% | 30.9 MiB/s | 506.0 KiB | 00m00s [105/186] Installing libusb1-0:1.0.29-5 100% | 21.6 MiB/s | 176.9 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [106/186] Installing tpm2-tss-0:4.1.3-9 100% | 272.2 MiB/s | 1.6 MiB | 00m00s [107/186] Installing ima-evm-utils-libs 100% | 60.4 MiB/s | 61.9 KiB | 00m00s [108/186] Installing gnupg2-gpg-agent-0 100% | 33.5 MiB/s | 686.5 KiB | 00m00s [109/186] Installing libxml2-0:2.12.10- 100% | 98.4 MiB/s | 1.8 MiB | 00m00s [110/186] Installing nettle-0:3.10.1-3. 100% | 259.6 MiB/s | 797.4 KiB | 00m00s [111/186] Installing gnutls-0:3.8.12-1. 100% | 339.6 MiB/s | 3.7 MiB | 00m00s [112/186] Installing bzip2-0:1.0.8-23.f 100% | 7.5 MiB/s | 99.5 KiB | 00m00s [113/186] Installing add-determinism-0: 100% | 121.7 MiB/s | 2.2 MiB | 00m00s [114/186] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [115/186] Installing cpio-0:2.15-9.fc44 100% | 69.0 MiB/s | 1.1 MiB | 00m00s [116/186] Installing ed-0:1.22.4-2.fc44 100% | 11.4 MiB/s | 151.4 KiB | 00m00s [117/186] Installing patch-0:2.8-4.fc44 100% | 17.1 MiB/s | 228.1 KiB | 00m00s [118/186] Installing lz4-libs-0:1.10.0- 100% | 154.6 MiB/s | 158.4 KiB | 00m00s [119/186] Installing libarchive-0:3.8.4 100% | 323.3 MiB/s | 993.1 KiB | 00m00s [120/186] Installing libgomp-0:16.0.1-0 100% | 280.2 MiB/s | 573.9 KiB | 00m00s [121/186] Installing libtool-ltdl-0:2.5 100% | 69.5 MiB/s | 71.1 KiB | 00m00s [122/186] Installing gdbm-libs-1:1.23-1 100% | 128.3 MiB/s | 131.3 KiB | 00m00s [123/186] Installing cyrus-sasl-lib-0:2 100% | 128.4 MiB/s | 2.3 MiB | 00m00s [124/186] Installing openldap-0:2.6.10- 100% | 218.5 MiB/s | 671.3 KiB | 00m00s [125/186] Installing gnupg2-dirmngr-0:2 100% | 31.1 MiB/s | 636.6 KiB | 00m00s [126/186] Installing gnupg2-0:2.4.9-5.f 100% | 216.9 MiB/s | 6.5 MiB | 00m00s [127/186] Installing rpm-sign-libs-0:6. 100% | 39.5 MiB/s | 40.5 KiB | 00m00s [128/186] Installing gpgverify-0:2.2-4. 100% | 0.0 B/s | 9.4 KiB | 00m00s [129/186] Installing jansson-0:2.14-4.f 100% | 88.2 MiB/s | 90.3 KiB | 00m00s [130/186] Installing libpkgconf-0:2.3.0 100% | 77.3 MiB/s | 79.2 KiB | 00m00s [131/186] Installing pkgconf-0:2.3.0-4. 100% | 6.8 MiB/s | 90.8 KiB | 00m00s [132/186] Installing pkgconf-pkg-config 100% | 147.8 KiB/s | 1.8 KiB | 00m00s [133/186] Installing xxhash-libs-0:0.8. 100% | 93.2 MiB/s | 95.4 KiB | 00m00s [134/186] Installing libnghttp2-0:1.68. 100% | 163.3 MiB/s | 167.3 KiB | 00m00s [135/186] Installing libnghttp3-0:1.15. 100% | 156.8 MiB/s | 160.6 KiB | 00m00s [136/186] Installing keyutils-libs-0:1. 100% | 54.3 MiB/s | 55.6 KiB | 00m00s [137/186] Installing libcom_err-0:1.47. 100% | 62.6 MiB/s | 64.1 KiB | 00m00s [138/186] Installing libverto-0:0.3.2-1 100% | 26.4 MiB/s | 27.1 KiB | 00m00s [139/186] Installing krb5-libs-0:1.21.3 100% | 295.6 MiB/s | 2.4 MiB | 00m00s [140/186] Installing libcbor-0:0.13.0-2 100% | 79.0 MiB/s | 80.9 KiB | 00m00s [141/186] Installing libfido2-0:1.16.0- 100% | 242.1 MiB/s | 247.9 KiB | 00m00s [142/186] Installing libssh-0:0.12.0-1. 100% | 234.8 MiB/s | 721.2 KiB | 00m00s [143/186] Installing libbrotli-0:1.2.0- 100% | 282.3 MiB/s | 867.3 KiB | 00m00s [144/186] Installing libcurl-0:8.18.0-4 100% | 331.4 MiB/s | 1.0 MiB | 00m00s [145/186] Installing curl-0:8.18.0-4.fc 100% | 21.4 MiB/s | 482.6 KiB | 00m00s [146/186] Installing rpm-0:6.0.1-3.fc45 100% | 77.3 MiB/s | 2.6 MiB | 00m00s [147/186] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [148/186] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [149/186] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [150/186] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [151/186] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.3 KiB | 00m00s [152/186] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [153/186] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [154/186] Installing elfutils-default-y 100% | 510.7 KiB/s | 2.0 KiB | 00m00s [155/186] Installing elfutils-libs-0:0. 100% | 233.4 MiB/s | 717.0 KiB | 00m00s [156/186] Installing elfutils-debuginfo 100% | 6.0 MiB/s | 86.0 KiB | 00m00s [157/186] Installing elfutils-0:0.194-3 100% | 147.9 MiB/s | 3.0 MiB | 00m00s [158/186] Installing binutils-0:2.46-1. 100% | 320.9 MiB/s | 27.3 MiB | 00m00s [159/186] Installing gdb-minimal-0:17.1 100% | 275.6 MiB/s | 14.3 MiB | 00m00s [160/186] Installing debugedit-0:5.2-6. 100% | 15.5 MiB/s | 221.6 KiB | 00m00s [161/186] Installing rpm-build-libs-0:6 100% | 270.7 MiB/s | 277.2 KiB | 00m00s [162/186] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [163/186] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [164/186] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [165/186] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [166/186] Installing package-notes-srpm 100% | 0.0 B/s | 2.1 KiB | 00m00s [167/186] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [168/186] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [169/186] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [170/186] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [171/186] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [172/186] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [173/186] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [174/186] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [175/186] Installing rpm-build-0:6.0.1- 100% | 15.6 MiB/s | 303.7 KiB | 00m00s [176/186] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [177/186] Installing redhat-rpm-config- 100% | 92.7 MiB/s | 189.9 KiB | 00m00s [178/186] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [179/186] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [180/186] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [181/186] Installing R-srpm-macros-0:1. 100% | 0.0 B/s | 4.2 KiB | 00m00s [182/186] Installing python-srpm-macros 100% | 51.7 MiB/s | 52.9 KiB | 00m00s [183/186] Installing rpm-plugin-selinux 100% | 0.0 B/s | 12.9 KiB | 00m00s [184/186] Installing which-0:2.23-4.fc4 100% | 6.0 MiB/s | 85.6 KiB | 00m00s [185/186] Installing shadow-utils-2:4.1 100% | 138.7 MiB/s | 4.0 MiB | 00m00s [186/186] Installing info-0:7.2-7.fc44. 100% | 48.7 KiB/s | 358.3 KiB | 00m07s Warning: skipped OpenPGP checks for 4 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: R-srpm-macros-1.3.4-3.fc44.noarch add-determinism-0.7.2-4.fc45.x86_64 alternatives-1.33-5.fc44.x86_64 ansible-srpm-macros-1-20.1.fc44.noarch audit-libs-4.1.3-1.fc44.x86_64 bash-5.3.9-3.fc44.x86_64 binutils-2.46-1.fc45.x86_64 build-reproducibility-srpm-macros-0.7.2-4.fc45.noarch bzip2-1.0.8-23.fc44.x86_64 bzip2-libs-1.0.8-23.fc44.x86_64 ca-certificates-2025.2.80_v9.0.304-5.fc44.noarch cmake-srpm-macros-4.2.3-1.fc45.noarch coreutils-9.10-1.fc45.x86_64 coreutils-common-9.10-1.fc45.x86_64 cpio-2.15-9.fc44.x86_64 crypto-policies-20251128-3.git19878fe.fc44.noarch curl-8.18.0-4.fc45.x86_64 cyrus-sasl-lib-2.1.28-35.fc44.x86_64 debugedit-5.2-6.fc44.x86_64 diffutils-3.12-5.fc44.x86_64 dwz-0.16-3.fc44.x86_64 ed-1.22.4-2.fc44.x86_64 efi-srpm-macros-6-6.fc44.noarch elfutils-0.194-3.fc44.x86_64 elfutils-debuginfod-client-0.194-3.fc44.x86_64 elfutils-default-yama-scope-0.194-3.fc44.noarch elfutils-libelf-0.194-3.fc44.x86_64 elfutils-libs-0.194-3.fc44.x86_64 fedora-gpg-keys-45-0.1.noarch fedora-release-45-0.1.noarch fedora-release-common-45-0.1.noarch fedora-release-identity-basic-45-0.1.noarch fedora-repos-45-0.1.noarch fedora-repos-rawhide-45-0.1.noarch file-5.46-9.fc44.x86_64 file-libs-5.46-9.fc44.x86_64 filesystem-3.18-52.fc44.x86_64 filesystem-srpm-macros-3.18-52.fc44.noarch findutils-4.10.0-7.fc44.x86_64 fonts-srpm-macros-5.0.0-2.fc44.noarch forge-srpm-macros-0.4.0-4.fc44.noarch fpc-srpm-macros-1.3-16.fc44.noarch gap-srpm-macros-2-2.fc44.noarch gawk-5.3.2-3.fc44.x86_64 gdb-minimal-17.1-2.fc44.x86_64 gdbm-libs-1.23-11.fc44.x86_64 ghc-srpm-macros-1.10-1.fc44.noarch glibc-2.43.9000-1.fc45.x86_64 glibc-common-2.43.9000-1.fc45.x86_64 glibc-gconv-extra-2.43.9000-1.fc45.x86_64 glibc-minimal-langpack-2.43.9000-1.fc45.x86_64 gmp-6.3.0-5.fc44.x86_64 gnat-srpm-macros-7-2.fc44.noarch gnulib-l10n-20241231-2.fc44.noarch gnupg2-2.4.9-5.fc44.x86_64 gnupg2-dirmngr-2.4.9-5.fc44.x86_64 gnupg2-gpg-agent-2.4.9-5.fc44.x86_64 gnupg2-gpgconf-2.4.9-5.fc44.x86_64 gnupg2-keyboxd-2.4.9-5.fc44.x86_64 gnupg2-verify-2.4.9-5.fc44.x86_64 gnutls-3.8.12-1.fc45.x86_64 go-srpm-macros-3.8.0-2.fc44.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-d924b10d3e810dabdd8b56b596e7e91491211fce-697c9899 gpgverify-2.2-4.fc44.noarch grep-3.12-3.fc44.x86_64 gzip-1.14-2.fc44.x86_64 ima-evm-utils-libs-1.6.2-8.fc44.x86_64 info-7.2-7.fc44.x86_64 jansson-2.14-4.fc44.x86_64 java-srpm-macros-1-8.fc44.noarch json-c-0.18-8.fc44.x86_64 kernel-srpm-macros-1.0-28.fc44.noarch keyutils-libs-1.6.3-7.fc44.x86_64 krb5-libs-1.21.3-12.fc44.x86_64 libacl-2.3.2-6.fc44.x86_64 libarchive-3.8.4-2.fc44.x86_64 libassuan-2.5.7-5.fc44.x86_64 libattr-2.5.2-8.fc44.x86_64 libblkid-2.41.3-12.fc44.x86_64 libbrotli-1.2.0-3.fc45.x86_64 libcap-2.77-2.fc44.x86_64 libcap-ng-0.9-7.fc44.x86_64 libcbor-0.13.0-2.fc44.x86_64 libcom_err-1.47.3-4.fc44.x86_64 libcurl-8.18.0-4.fc45.x86_64 libeconf-0.7.9-3.fc44.x86_64 libevent-2.1.12-17.fc44.x86_64 libfdisk-2.41.3-12.fc44.x86_64 libffi-3.5.2-2.fc44.x86_64 libfido2-1.16.0-5.fc44.x86_64 libfsverity-1.6-4.fc44.x86_64 libgcc-16.0.1-0.7.fc45.x86_64 libgcrypt-1.11.2-1.fc44.x86_64 libgomp-16.0.1-0.7.fc45.x86_64 libgpg-error-1.58-2.fc44.x86_64 libidn2-2.3.8-3.fc44.x86_64 libksba-1.6.7-5.fc44.x86_64 liblastlog2-2.41.3-12.fc44.x86_64 libmount-2.41.3-12.fc44.x86_64 libnghttp2-1.68.0-3.fc44.x86_64 libnghttp3-1.15.0-1.fc44.x86_64 libpkgconf-2.3.0-4.fc44.x86_64 libpsl-0.21.5-7.fc44.x86_64 libselinux-3.10-1.fc45.x86_64 libselinux-utils-3.10-1.fc45.x86_64 libsemanage-3.10-1.fc44.x86_64 libsepol-3.10-1.fc44.x86_64 libsmartcols-2.41.3-12.fc44.x86_64 libssh-0.12.0-1.fc45.x86_64 libssh-config-0.12.0-1.fc45.noarch libstdc++-16.0.1-0.7.fc45.x86_64 libtasn1-4.20.0-3.fc44.x86_64 libtool-ltdl-2.5.4-10.fc44.x86_64 libunistring-1.1-11.fc44.x86_64 libusb1-1.0.29-5.fc44.x86_64 libuuid-2.41.3-12.fc44.x86_64 libverto-0.3.2-12.fc44.x86_64 libxcrypt-4.5.2-3.fc44.x86_64 libxml2-2.12.10-6.fc44.x86_64 libzstd-1.5.7-5.fc44.x86_64 linkdupes-0.7.2-4.fc45.x86_64 lua-srpm-macros-1-17.fc44.noarch lua5.4-libs-5.5.0-1.fc45.x86_64 lz4-libs-1.10.0-4.fc44.x86_64 mpfr-4.2.2-3.fc44.x86_64 ncurses-base-6.6-1.fc44.noarch ncurses-libs-6.6-1.fc44.x86_64 nettle-3.10.1-3.fc44.x86_64 ngtcp2-1.19.0-2.fc44.x86_64 ngtcp2-crypto-ossl-1.19.0-2.fc44.x86_64 npth-1.8-4.fc44.x86_64 ocaml-srpm-macros-11-3.fc44.noarch openblas-srpm-macros-2-21.fc44.noarch openldap-2.6.10-7.fc44.x86_64 openssl-libs-3.5.5-1.fc44.x86_64 p11-kit-0.26.2-1.fc45.x86_64 p11-kit-trust-0.26.2-1.fc45.x86_64 package-notes-srpm-macros-0.17-3.fc45.noarch pam-libs-1.7.2-1.fc44.x86_64 patch-2.8-4.fc44.x86_64 pcre2-10.47-1.fc44.1.x86_64 pcre2-syntax-10.47-1.fc44.1.noarch perl-srpm-macros-1-61.fc44.noarch pkgconf-2.3.0-4.fc44.x86_64 pkgconf-m4-2.3.0-4.fc44.noarch pkgconf-pkg-config-2.3.0-4.fc44.x86_64 policycoreutils-3.10-1.fc45.x86_64 popt-1.19-10.fc44.x86_64 publicsuffix-list-dafsa-20260116-1.fc44.noarch pyproject-srpm-macros-1.18.6-2.fc44.noarch python-srpm-macros-3.14-10.fc44.noarch qt5-srpm-macros-5.15.18-2.fc44.noarch qt6-srpm-macros-6.10.2-1.fc45.noarch readline-8.3-4.fc44.x86_64 redhat-rpm-config-343-19.fc44.noarch rpm-6.0.1-3.fc45.x86_64 rpm-build-6.0.1-3.fc45.x86_64 rpm-build-libs-6.0.1-3.fc45.x86_64 rpm-libs-6.0.1-3.fc45.x86_64 rpm-plugin-selinux-6.0.1-3.fc45.x86_64 rpm-sequoia-1.10.0-2.fc44.x86_64 rpm-sign-libs-6.0.1-3.fc45.x86_64 rust-srpm-macros-28.4-3.fc44.noarch sed-4.9-8.fc45.x86_64 selinux-policy-42.23-1.fc44.noarch selinux-policy-targeted-42.23-1.fc44.noarch setup-2.15.0-28.fc44.noarch shadow-utils-4.19.0-6.fc44.x86_64 sqlite-libs-3.51.2-1.fc44.x86_64 systemd-libs-259.1-1.fc45.x86_64 systemd-standalone-sysusers-259.1-1.fc45.x86_64 tar-1.35-8.fc44.x86_64 tpm2-tss-4.1.3-9.fc44.x86_64 tree-sitter-srpm-macros-0.4.2-2.fc44.noarch unzip-6.0-69.fc44.x86_64 util-linux-2.41.3-12.fc44.x86_64 util-linux-core-2.41.3-12.fc44.x86_64 which-2.23-4.fc44.x86_64 xxhash-libs-0.8.3-4.fc44.x86_64 xz-5.8.2-2.fc44.x86_64 xz-libs-5.8.2-2.fc44.x86_64 zig-srpm-macros-1-8.fc44.noarch zip-3.0-45.fc44.x86_64 zlib-ng-compat-2.3.3-2.fc45.x86_64 zstd-1.5.7-5.fc44.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.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_64-1770926021.807988/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-1sfby99c/pymol/pymol.spec) Config(child) 0 minutes 18 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-3.1.0-14.fc45.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1770926021.807988/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1770926021.807988/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_64-1770926021.807988/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-6.0.1-3.fc45.x86_64 rpm-sequoia-1.10.0-2.fc44.x86_64 dnf5-5.3.0.0-7.fc44.x86_64 dnf5-plugins-5.3.0.0-7.fc44.x86_64 Finish: chroot init Start: build phase for pymol-3.1.0-14.fc45.src.rpm Start: build setup for pymol-3.1.0-14.fc45.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.src.rpm Updating and loading repositories: Copr repository 100% | 24.7 KiB/s | 1.5 KiB | 00m00s fedora 100% | 178.1 KiB/s | 23.0 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: catch2-devel x86_64 0:2.13.10-9.fc44 fedora 952.9 KiB desktop-file-utils x86_64 0:0.28-5.fc44 fedora 218.0 KiB fdupes x86_64 1:2.4.0-3.fc44 fedora 117.9 KiB freeglut-devel x86_64 0:3.8.0-2.fc44 fedora 2.3 MiB freetype-devel x86_64 0:2.14.1-2.fc44 fedora 8.6 MiB gcc x86_64 0:16.0.1-0.7.fc45 fedora 120.8 MiB gcc-c++ x86_64 0:16.0.1-0.7.fc45 fedora 46.3 MiB glew-devel x86_64 0:2.2.0-12.fc44 fedora 1.8 MiB glm-devel noarch 0:1.0.1-6.fc44 fedora 2.1 MiB libappstream-glib x86_64 0:0.8.3-5.fc44 fedora 1.4 MiB libpng-devel x86_64 2:1.6.53-2.fc44 fedora 886.4 KiB libxml2-devel x86_64 0:2.12.10-6.fc44 fedora 3.4 MiB mesa-libGL-devel x86_64 0:26.0.0~rc3-1.fc45 fedora 80.8 KiB mmtf-cpp-devel x86_64 0:1.1.0-9.fc44 fedora 114.4 KiB msgpack-devel x86_64 0:3.1.0-23.fc44 fedora 5.1 MiB netcdf-devel x86_64 0:4.9.3-2.fc44 fedora 397.7 KiB pyproject-rpm-macros noarch 0:1.18.6-2.fc44 fedora 115.6 KiB python3-devel x86_64 0:3.14.3-1.fc45 fedora 1.9 MiB 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371.8 KiB qt6-qtsvg x86_64 0:6.10.2-1.fc45 fedora 905.8 KiB qt6-qttools x86_64 0:6.10.2-1.fc45 fedora 902.2 KiB qt6-qttools-common noarch 0:6.10.2-1.fc45 fedora 7.5 KiB qt6-qttools-libs-designer x86_64 0:6.10.2-1.fc45 fedora 6.0 MiB qt6-qttools-libs-designercomponents x86_64 0:6.10.2-1.fc45 fedora 3.4 MiB qt6-qttools-libs-help x86_64 0:6.10.2-1.fc45 fedora 622.8 KiB qt6-qtwebchannel x86_64 0:6.10.2-1.fc45 fedora 440.3 KiB qt6-qtwebengine x86_64 0:6.10.2-1.fc45 fedora 269.6 MiB qt6-qtwebsockets x86_64 0:6.10.2-1.fc45 fedora 324.4 KiB qt6-qtwebview x86_64 0:6.10.2-1.fc45 fedora 302.3 KiB qt6-rpm-macros noarch 0:6.10.2-1.fc45 fedora 3.0 KiB rav1e-libs x86_64 0:0.8.1-3.fc44 fedora 3.1 MiB re2 x86_64 2:20251105-4.fc44 fedora 606.8 KiB rhash x86_64 0:1.4.5-4.fc44 fedora 354.8 KiB samba-client-libs x86_64 2:4.24.0-0.2.rc1.fc44 fedora 11.2 MiB samba-common noarch 2:4.24.0-0.2.rc1.fc44 fedora 199.6 KiB samba-core-libs x86_64 2:4.24.0-0.2.rc1.fc44 fedora 1.7 MiB samba-ndr-libs x86_64 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x86_64 0:0.1.3-24.fc44 fedora 157.8 KiB vulkan-headers noarch 0:1.4.328.1-2.fc44 fedora 31.8 MiB vulkan-loader x86_64 0:1.4.328.1-2.fc44 fedora 565.3 KiB vulkan-loader-devel x86_64 0:1.4.328.1-2.fc44 fedora 8.0 KiB webrtc-audio-processing x86_64 0:2.1-5.fc44 fedora 1.1 MiB xcb-util x86_64 0:0.4.1-9.fc44 fedora 26.1 KiB xcb-util-cursor x86_64 0:0.1.6-2.fc44 fedora 23.1 KiB xcb-util-image x86_64 0:0.4.1-9.fc44 fedora 22.0 KiB xcb-util-keysyms x86_64 0:0.4.1-9.fc44 fedora 16.6 KiB xcb-util-renderutil x86_64 0:0.3.10-9.fc44 fedora 24.2 KiB xcb-util-wm x86_64 0:0.4.2-9.fc44 fedora 81.0 KiB xevd-libs x86_64 0:0.5.0-6.fc44 fedora 379.9 KiB xeve-libs x86_64 0:0.5.1-6.fc44 fedora 904.7 KiB xkeyboard-config noarch 0:2.46-2.fc44 fedora 6.4 MiB xml-common noarch 0:0.6.3-68.fc44 fedora 78.4 KiB xorg-x11-proto-devel noarch 0:2025.1-2.fc44 fedora 1.8 MiB xprop x86_64 0:1.2.8-5.fc44 fedora 54.5 KiB xvidcore x86_64 0:1.3.7-19.fc44 fedora 878.3 KiB xz-devel x86_64 1:5.8.2-2.fc44 fedora 258.8 KiB zeromq x86_64 0:4.3.5-22.fc43 fedora 894.1 KiB zlib-ng-compat-devel x86_64 0:2.3.3-2.fc45 fedora 107.0 KiB zvbi x86_64 0:0.2.44-3.fc44 fedora 1.2 MiB Transaction Summary: Installing: 536 packages Total size of inbound packages is 580 MiB. Need to download 559 MiB. After this operation, 2 GiB extra will be used (install 2 GiB, remove 0 B). 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libtextstyle-0:0.2 100% | 207.2 MiB/s | 212.2 KiB | 00m00s [ 55/538] Installing gettext-libs-0:0.2 100% | 322.4 MiB/s | 2.3 MiB | 00m00s [ 56/538] Installing libquadmath-0:16.0 100% | 35.5 MiB/s | 327.2 KiB | 00m00s [ 57/538] Installing openssl-devel-1:3. 100% | 62.4 MiB/s | 5.4 MiB | 00m00s [ 58/538] Installing ngtcp2-devel-0:1.1 100% | 69.2 MiB/s | 283.6 KiB | 00m00s [ 59/538] Installing kernel-headers-0:6 100% | 195.2 MiB/s | 7.0 MiB | 00m00s [ 60/538] Installing glibc-devel-0:2.43 100% | 170.5 MiB/s | 2.4 MiB | 00m00s [ 61/538] Installing libxcrypt-devel-0: 100% | 6.5 MiB/s | 33.3 KiB | 00m00s [ 62/538] Installing libwbclient-2:4.24 100% | 70.2 MiB/s | 71.9 KiB | 00m00s [ 63/538] Installing mpg123-libs-0:1.32 100% | 269.6 MiB/s | 828.3 KiB | 00m00s [ 64/538] Installing pixman-0:0.46.2-3. 100% | 234.1 MiB/s | 719.3 KiB | 00m00s [ 65/538] Installing lzo-0:2.10-16.fc44 100% | 172.3 MiB/s | 176.4 KiB | 00m00s [ 66/538] Installing spirv-tools-libs-0 100% | 361.7 MiB/s | 5.8 MiB | 00m00s [ 67/538] Installing mesa-filesystem-0: 100% | 4.2 MiB/s | 4.3 KiB | 00m00s [ 68/538] Installing abseil-cpp-0:20260 100% | 235.5 MiB/s | 2.6 MiB | 00m00s [ 69/538] Installing jsoncpp-0:1.9.6-3. 100% | 280.4 MiB/s | 287.1 KiB | 00m00s [ 70/538] Installing libdvdread-0:6.1.3 100% | 161.8 MiB/s | 165.7 KiB | 00m00s [ 71/538] Installing svt-av1-libs-0:3.1 100% | 374.1 MiB/s | 5.6 MiB | 00m00s [ 72/538] Installing rav1e-libs-0:0.8.1 100% | 385.4 MiB/s | 3.1 MiB | 00m00s [ 73/538] Installing libvpl-1:2.16.0-2. 100% | 215.2 MiB/s | 440.7 KiB | 00m00s [ 74/538] Installing liblc3-0:1.1.3-7.f 100% | 171.5 MiB/s | 175.7 KiB | 00m00s [ 75/538] Installing lame-libs-0:3.100- 100% | 400.8 MiB/s | 1.2 MiB | 00m00s [ 76/538] Installing gsm-0:1.0.23-2.fc4 100% | 65.2 MiB/s | 66.8 KiB | 00m00s [ 77/538] Installing fdk-aac-free-0:2.0 100% | 307.5 MiB/s | 629.8 KiB | 00m00s [ 78/538] Installing vulkan-loader-0:1. 100% | 277.3 MiB/s | 567.9 KiB | 00m00s [ 79/538] Installing libunwind-0:1.8.3- 100% | 192.8 MiB/s | 197.4 KiB | 00m00s [ 80/538] Installing libevdev-0:1.13.6- 100% | 17.8 MiB/s | 91.0 KiB | 00m00s [ 81/538] Installing xml-common-0:0.6.3 100% | 79.2 MiB/s | 81.1 KiB | 00m00s [ 82/538] Installing qt5-qttools-common 100% | 0.0 B/s | 7.9 KiB | 00m00s [ 83/538] Installing libxslt-0:1.1.43-6 100% | 29.0 MiB/s | 474.9 KiB | 00m00s [ 84/538] Installing mtdev-0:1.1.6-12.f 100% | 29.6 MiB/s | 30.3 KiB | 00m00s [ 85/538] Installing double-conversion- 100% | 101.1 MiB/s | 103.5 KiB | 00m00s [ 86/538] Installing libgfortran-0:16.0 100% | 378.9 MiB/s | 3.4 MiB | 00m00s [ 87/538] Installing hdf5-0:1.14.6-7.fc 100% | 198.1 MiB/s | 6.5 MiB | 00m00s [ 88/538] Installing libseccomp-0:2.6.0 100% | 221.4 MiB/s | 226.7 KiB | 00m00s [ 89/538] Installing graphite2-0:1.3.14 100% | 13.5 MiB/s | 193.6 KiB | 00m00s [ 90/538] Installing harfbuzz-0:12.3.2- 100% | 342.5 MiB/s | 2.7 MiB | 00m00s [ 91/538] Installing freetype-0:2.14.1- 100% | 300.7 MiB/s | 923.9 KiB | 00m00s [ 92/538] Installing libXau-0:1.0.12-4. 100% | 72.6 MiB/s | 74.3 KiB | 00m00s [ 93/538] Installing libxcb-0:1.17.0-7. 100% | 215.5 MiB/s | 1.1 MiB | 00m00s [ 94/538] Installing xcb-util-renderuti 100% | 25.1 MiB/s | 25.7 KiB | 00m00s [ 95/538] Installing xcb-util-keysyms-0 100% | 0.0 B/s | 17.7 KiB | 00m00s [ 96/538] Installing xcb-util-wm-0:0.4. 100% | 81.0 MiB/s | 83.0 KiB | 00m00s [ 97/538] Installing make-1:4.4.1-12.fc 100% | 100.0 MiB/s | 1.8 MiB | 00m00s [ 98/538] Installing pcre2-utf32-0:10.4 100% | 203.1 MiB/s | 623.9 KiB | 00m00s [ 99/538] Installing pcre2-devel-0:10.4 100% | 106.0 MiB/s | 2.1 MiB | 00m00s [100/538] Installing emacs-filesystem-1 100% | 0.0 B/s | 812.0 B | 00m00s [101/538] Installing xcb-util-0:0.4.1-9 100% | 0.0 B/s | 27.5 KiB | 00m00s [102/538] Installing xcb-util-image-0:0 100% | 22.9 MiB/s | 23.5 KiB | 00m00s [103/538] Installing xcb-util-cursor-0: 100% | 23.9 MiB/s | 24.5 KiB | 00m00s [104/538] Installing libXau-devel-0:1.0 100% | 1.5 MiB/s | 9.1 KiB | 00m00s [105/538] Installing libxcb-devel-0:1.1 100% | 81.5 MiB/s | 3.0 MiB | 00m00s [106/538] Installing libraqm-0:0.10.1-4 100% | 32.8 MiB/s | 33.6 KiB | 00m00s [107/538] Installing harfbuzz-icu-0:12. 100% | 0.0 B/s | 16.1 KiB | 00m00s [108/538] Installing graphite2-devel-0: 100% | 16.5 MiB/s | 50.8 KiB | 00m00s [109/538] Installing iso-codes-0:4.20.1 100% | 308.7 MiB/s | 22.5 MiB | 00m00s [110/538] Installing libdvdnav-0:6.1.1- 100% | 114.9 MiB/s | 117.6 KiB | 00m00s [111/538] Installing openxr-libs-0:1.1. 100% | 274.9 MiB/s | 281.5 KiB | 00m00s [112/538] Installing re2-2:20251105-4.f 100% | 296.9 MiB/s | 608.2 KiB | 00m00s [113/538] Installing webrtc-audio-proce 100% | 266.6 MiB/s | 1.1 MiB | 00m00s [114/538] Installing libshaderc-0:2025. 100% | 366.9 MiB/s | 3.7 MiB | 00m00s [115/538] Installing pixman-devel-0:0.4 100% | 0.0 B/s | 56.9 KiB | 00m00s [116/538] Installing libopenmpt-0:0.8.4 100% | 310.3 MiB/s | 1.9 MiB | 00m00s [117/538] Installing ngtcp2-crypto-ossl 100% | 0.0 B/s | 8.1 KiB | 00m00s [118/538] Installing pyproject-rpm-macr 100% | 114.8 MiB/s | 117.5 KiB | 00m00s [119/538] Installing blosc-0:1.21.6-10. 100% | 125.9 MiB/s | 128.9 KiB | 00m00s [120/538] Installing abattis-cantarell- 100% | 189.9 MiB/s | 194.4 KiB | 00m00s [121/538] Installing hdf-libs-0:4.3.0-5 100% | 345.7 MiB/s | 708.0 KiB | 00m00s [122/538] Installing libnsl2-0:2.0.1-5. 100% | 57.5 MiB/s | 58.8 KiB | 00m00s [123/538] Installing libgusb-0:0.4.9-5. 100% | 155.9 MiB/s | 159.6 KiB | 00m00s [124/538] Installing colord-libs-0:1.4. 100% | 271.3 MiB/s | 833.4 KiB | 00m00s [125/538] Installing cpp-0:16.0.1-0.7.f 100% | 332.0 MiB/s | 42.2 MiB | 00m00s [126/538] Installing libaec-devel-0:1.1 100% | 23.3 MiB/s | 23.9 KiB | 00m00s [127/538] Installing avahi-glib-0:0.9~r 100% | 0.0 B/s | 20.3 KiB | 00m00s [128/538] Installing mesa-libGLU-0:9.0. 100% | 180.9 MiB/s | 370.6 KiB | 00m00s [129/538] Installing nss-softokn-freebl 100% | 325.8 MiB/s | 1.0 MiB | 00m00s [130/538] Installing nss-softokn-0:3.12 100% | 404.5 MiB/s | 2.0 MiB | 00m00s [131/538] Installing nss-0:3.120.0-1.fc 100% | 179.5 MiB/s | 2.0 MiB | 00m00s [132/538] Installing nss-sysinit-0:3.12 100% | 1.3 MiB/s | 19.1 KiB | 00m00s [133/538] Installing libmng-0:2.0.3-25. 100% | 271.6 MiB/s | 556.3 KiB | 00m00s [134/538] Installing flac-libs-0:1.5.0- 100% | 307.6 MiB/s | 630.1 KiB | 00m00s [135/538] Installing libsndfile-0:1.2.2 100% | 269.3 MiB/s | 551.6 KiB | 00m00s [136/538] Installing aribb24-0:1.0.3^20 100% | 82.4 MiB/s | 84.4 KiB | 00m00s [137/538] Installing zvbi-0:0.2.44-3.fc 100% | 50.3 MiB/s | 1.2 MiB | 00m00s [138/538] Installing libicu-devel-0:77. 100% | 181.6 MiB/s | 5.1 MiB | 00m00s [139/538] Installing jasper-libs-0:4.2. 100% | 171.5 MiB/s | 351.2 KiB | 00m00s [140/538] Installing graphene-0:1.10.8- 100% | 156.3 MiB/s | 160.0 KiB | 00m00s [141/538] Installing libcloudproviders- 100% | 123.3 MiB/s | 126.3 KiB | 00m00s [142/538] Installing gdbm-1:1.23-11.fc4 100% | 30.3 MiB/s | 464.7 KiB | 00m00s [143/538] Installing cracklib-0:2.9.11- 100% | 14.5 MiB/s | 237.0 KiB | 00m00s [144/538] Installing libpwquality-0:1.4 100% | 24.2 MiB/s | 421.0 KiB | 00m00s [145/538] Installing authselect-libs-0: 100% | 88.5 MiB/s | 906.2 KiB | 00m00s [146/538] Installing annobin-docs-0:13. 100% | 16.3 MiB/s | 100.3 KiB | 00m00s >>> Running sysusers scriptlet: dbus-common-1:1.16.0-8.fc44.noarch >>> Finished sysusers scriptlet: dbus-common-1:1.16.0-8.fc44.noarch >>> Scriptlet output: >>> Creating group 'dbus' with GID 81. >>> Creating user 'dbus' (System Message Bus) with UID 81 and GID 81. >>> [147/538] Installing dbus-common-1:1.16 100% | 903.4 KiB/s | 13.6 KiB | 00m00s [148/538] Installing dbus-broker-0:37-8 100% | 18.5 MiB/s | 397.5 KiB | 00m00s [149/538] Installing dbus-1:1.16.0-8.fc 100% | 0.0 B/s | 124.0 B | 00m00s [150/538] Installing gupnp-0:1.6.9-3.fc 100% | 153.2 MiB/s | 313.7 KiB | 00m00s [151/538] Installing gupnp-igd-0:1.6.0- 100% | 66.8 MiB/s | 68.4 KiB | 00m00s [152/538] Installing libnice-0:0.1.23-2 100% | 33.4 MiB/s | 512.8 KiB | 00m00s [153/538] Installing systemd-shared-0:2 100% | 164.3 MiB/s | 5.4 MiB | 00m00s >>> Running sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Finished sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Scriptlet output: >>> Creating group 'empower' with GID 999. >>> >>> Running sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Finished sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Scriptlet output: >>> Creating group 'systemd-journal' with GID 190. >>> >>> Running sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Finished sysusers scriptlet: systemd-0:259.1-1.fc45.x86_64 >>> Scriptlet output: >>> Creating group 'systemd-oom' with GID 998. >>> Creating user 'systemd-oom' (systemd Userspace OOM Killer) with UID 998 and GID 998. >>> [154/538] Installing systemd-0:259.1-1. 100% | 83.2 MiB/s | 13.1 MiB | 00m00s >>> Running sysusers scriptlet: samba-common-2:4.24.0-0.2.rc1.fc44.noarch >>> Finished sysusers scriptlet: samba-common-2:4.24.0-0.2.rc1.fc44.noarch >>> Scriptlet output: >>> Creating group 'printadmin' with GID 997. >>> [155/538] Installing samba-common-2:4.2 100% | 24.8 MiB/s | 203.1 KiB | 00m00s [156/538] Installing samba-core-libs-2: 100% | 279.8 MiB/s | 1.7 MiB | 00m00s [157/538] Installing samba-ndr-libs-2:4 100% | 360.1 MiB/s | 4.7 MiB | 00m00s [158/538] Installing libblkid-devel-0:2 100% | 45.0 MiB/s | 46.0 KiB | 00m00s [159/538] Installing lzo-minilzo-0:2.10 100% | 36.9 MiB/s | 37.8 KiB | 00m00s [160/538] Installing lzo-devel-0:2.10-1 100% | 210.2 MiB/s | 215.3 KiB | 00m00s [161/538] Installing gettext-envsubst-0 100% | 5.3 MiB/s | 76.0 KiB | 00m00s [162/538] Installing gettext-runtime-0: 100% | 41.2 MiB/s | 718.0 KiB | 00m00s [163/538] Installing gettext-0:0.26-4.f 100% | 329.7 MiB/s | 12.9 MiB | 00m00s [164/538] Installing sysprof-capture-de 100% | 398.4 MiB/s | 816.0 KiB | 00m00s [165/538] Installing libffi-devel-0:3.5 100% | 0.0 B/s | 35.6 KiB | 00m00s [166/538] Installing vim-filesystem-2:9 100% | 4.6 MiB/s | 4.7 KiB | 00m00s [167/538] Installing rhash-0:1.4.5-4.fc 100% | 25.1 MiB/s | 360.1 KiB | 00m00s [168/538] Installing libuv-1:1.51.0-3.f 100% | 285.9 MiB/s | 585.6 KiB | 00m00s [169/538] Installing bzip2-devel-0:1.0. 100% | 303.5 MiB/s | 310.7 KiB | 00m00s [170/538] Installing libatomic-0:16.0.1 100% | 45.5 MiB/s | 46.6 KiB | 00m00s [171/538] Installing gcc-0:16.0.1-0.7.f 100% | 384.8 MiB/s | 120.8 MiB | 00m00s [172/538] Installing libquadmath-devel- 100% | 23.1 MiB/s | 23.6 KiB | 00m00s [173/538] Installing gcc-gfortran-0:16. 100% | 328.3 MiB/s | 44.7 MiB | 00m00s [174/538] Installing hdf5-devel-0:1.14. 100% | 145.2 MiB/s | 3.3 MiB | 00m00s [175/538] Installing libstdc++-devel-0: 100% | 452.1 MiB/s | 38.9 MiB | 00m00s [176/538] Installing gcc-c++-0:16.0.1-0 100% | 342.9 MiB/s | 46.3 MiB | 00m00s [177/538] Installing libverto-devel-0:0 100% | 0.0 B/s | 26.4 KiB | 00m00s [178/538] Installing libcom_err-devel-0 100% | 1.4 MiB/s | 18.3 KiB | 00m00s [179/538] Installing keyutils-libs-deve 100% | 53.9 MiB/s | 55.2 KiB | 00m00s [180/538] Installing libsepol-devel-0:3 100% | 63.0 MiB/s | 129.0 KiB | 00m00s [181/538] Installing libselinux-devel-0 100% | 51.1 MiB/s | 156.9 KiB | 00m00s [182/538] Installing libmount-devel-0:2 100% | 65.0 MiB/s | 66.5 KiB | 00m00s [183/538] Installing publicsuffix-list- 100% | 335.2 MiB/s | 343.2 KiB | 00m00s [184/538] Installing libpsl-devel-0:0.2 100% | 110.9 MiB/s | 113.5 KiB | 00m00s [185/538] Installing libnghttp3-devel-0 100% | 0.0 B/s | 108.2 KiB | 00m00s [186/538] Installing libnghttp2-devel-0 100% | 282.3 MiB/s | 289.1 KiB | 00m00s [187/538] Installing libidn2-devel-0:2. 100% | 153.0 MiB/s | 156.7 KiB | 00m00s [188/538] Installing libkadm5-0:1.21.3- 100% | 214.6 MiB/s | 219.8 KiB | 00m00s [189/538] Installing krb5-devel-0:1.21. 100% | 46.6 MiB/s | 715.2 KiB | 00m00s [190/538] Installing libssh-devel-0:0.1 100% | 201.4 MiB/s | 206.2 KiB | 00m00s [191/538] Installing brotli-0:1.2.0-3.f 100% | 2.6 MiB/s | 34.3 KiB | 00m00s [192/538] Installing brotli-devel-0:1.2 100% | 33.4 MiB/s | 68.4 KiB | 00m00s [193/538] Installing libcurl-devel-0:8. 100% | 56.2 MiB/s | 1.5 MiB | 00m00s [194/538] Installing mariadb-connector- 100% | 0.0 B/s | 1.0 KiB | 00m00s [195/538] Installing mariadb-connector- 100% | 172.1 MiB/s | 528.7 KiB | 00m00s [196/538] Installing libtommath-0:1.3.1 100% | 128.3 MiB/s | 131.4 KiB | 00m00s [197/538] Installing libfbclient2-0:5.0 100% | 363.8 MiB/s | 3.3 MiB | 00m00s [198/538] Installing libpq-0:18.0-4.fc4 100% | 253.9 MiB/s | 1.0 MiB | 00m00s [199/538] Installing unixODBC-0:2.3.14- 100% | 59.7 MiB/s | 1.0 MiB | 00m00s [200/538] Installing python-pip-wheel-0 100% | 611.4 MiB/s | 1.2 MiB | 00m00s [201/538] Installing clang-resource-fil 100% | 0.0 B/s | 16.7 KiB | 00m00s [202/538] Installing ncurses-0:6.6-1.fc 100% | 27.4 MiB/s | 618.0 KiB | 00m00s [203/538] Installing groff-base-0:1.23. 100% | 111.3 MiB/s | 3.9 MiB | 00m00s [204/538] Installing perl-Digest-0:1.20 100% | 36.2 MiB/s | 37.1 KiB | 00m00s [205/538] Installing perl-Digest-MD5-0: 100% | 60.0 MiB/s | 61.5 KiB | 00m00s [206/538] Installing perl-FileHandle-0: 100% | 0.0 B/s | 9.8 KiB | 00m00s [207/538] Installing perl-B-0:1.89-522. 100% | 246.4 MiB/s | 504.6 KiB | 00m00s [208/538] Installing perl-libnet-0:3.15 100% | 143.9 MiB/s | 294.7 KiB | 00m00s [209/538] Installing perl-Data-Dumper-0 100% | 114.7 MiB/s | 117.4 KiB | 00m00s [210/538] Installing perl-MIME-Base32-0 100% | 31.4 MiB/s | 32.2 KiB | 00m00s [211/538] Installing perl-URI-0:5.34-3. 100% | 91.7 MiB/s | 281.8 KiB | 00m00s [212/538] Installing perl-AutoLoader-0: 100% | 0.0 B/s | 21.0 KiB | 00m00s [213/538] Installing perl-IO-Socket-IP- 100% | 99.8 MiB/s | 102.2 KiB | 00m00s [214/538] Installing perl-IO-Socket-SSL 100% | 236.9 MiB/s | 727.6 KiB | 00m00s [215/538] Installing perl-Net-SSLeay-0: 100% | 269.4 MiB/s | 1.3 MiB | 00m00s [216/538] Installing perl-locale-0:1.13 100% | 0.0 B/s | 6.5 KiB | 00m00s [217/538] Installing perl-if-0:0.61.000 100% | 0.0 B/s | 6.2 KiB | 00m00s [218/538] Installing perl-Text-Tabs+Wra 100% | 0.0 B/s | 23.9 KiB | 00m00s [219/538] Installing perl-Pod-Escapes-1 100% | 0.0 B/s | 25.9 KiB | 00m00s [220/538] Installing perl-Time-Local-2: 100% | 68.9 MiB/s | 70.6 KiB | 00m00s [221/538] Installing perl-Time-HiRes-4: 100% | 114.9 MiB/s | 117.7 KiB | 00m00s [222/538] Installing perl-File-Path-0:2 100% | 0.0 B/s | 64.5 KiB | 00m00s [223/538] Installing perl-HTTP-Tiny-0:0 100% | 155.9 MiB/s | 159.7 KiB | 00m00s [224/538] Installing perl-Pod-Simple-1: 100% | 187.1 MiB/s | 574.9 KiB | 00m00s [225/538] Installing perl-POSIX-0:2.23- 100% | 225.2 MiB/s | 230.6 KiB | 00m00s [226/538] Installing perl-IPC-Open3-0:1 100% | 0.0 B/s | 28.5 KiB | 00m00s [227/538] Installing perl-File-Temp-1:0 100% | 161.6 MiB/s | 165.5 KiB | 00m00s [228/538] Installing perl-Term-Cap-0:1. 100% | 29.9 MiB/s | 30.6 KiB | 00m00s [229/538] Installing perl-Term-ANSIColo 100% | 96.9 MiB/s | 99.2 KiB | 00m00s [230/538] 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Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.src.rpm Updating and loading repositories: Copr repository 100% | 32.6 KiB/s | 1.5 KiB | 00m00s fedora 100% | 117.8 KiB/s | 23.0 KiB | 00m00s Repositories loaded. Nothing to do. Package "catch2-devel-2.13.10-9.fc44.x86_64" is already installed. Package "desktop-file-utils-0.28-5.fc44.x86_64" is already installed. Package "fdupes-1:2.4.0-3.fc44.x86_64" is already installed. Package "freeglut-devel-3.8.0-2.fc44.x86_64" is already installed. Package "freetype-devel-2.14.1-2.fc44.x86_64" is already installed. Package "gcc-16.0.1-0.7.fc45.x86_64" is already installed. Package "gcc-c++-16.0.1-0.7.fc45.x86_64" is already installed. Package "glew-devel-2.2.0-12.fc44.x86_64" is already installed. Package "glm-devel-1.0.1-6.fc44.noarch" is already installed. Package "mesa-libGL-devel-26.0.0~rc3-1.fc45.x86_64" is already installed. Package "libappstream-glib-0.8.3-5.fc44.x86_64" is already installed. Package "libpng-devel-2:1.6.53-2.fc44.x86_64" is already installed. Package "libxml2-devel-2.12.10-6.fc44.x86_64" is already installed. Package "mmtf-cpp-devel-1.1.0-9.fc44.x86_64" is already installed. Package "msgpack-devel-3.1.0-23.fc44.x86_64" is already installed. Package "netcdf-devel-4.9.3-2.fc44.x86_64" is already installed. Package "pyproject-rpm-macros-1.18.6-2.fc44.noarch" is already installed. Package "python3-devel-3.14.3-1.fc45.x86_64" is already installed. Package "python3-pillow-12.1.1-1.fc45.x86_64" is already installed. Package "python3-pyside6-devel-6.10.2-1.fc45.x86_64" is already installed. Package "python3-pytest-8.4.2-2.fc44.noarch" is already installed. Package "python3-qt5-devel-5.15.12-0.2.fc44.x86_64" is already installed. Finish: build setup for pymol-3.1.0-14.fc45.src.rpm Start: rpmbuild pymol-3.1.0-14.fc45.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.Br8OdI Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.JCGyWB + 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.hlgvIg + 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/.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/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + 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/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.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-3.1.0-14.fc45.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: Copr repository 100% | 85.1 KiB/s | 1.5 KiB | 00m00s fedora 100% | 185.3 KiB/s | 23.0 KiB | 00m00s Repositories loaded. Package "catch2-devel-2.13.10-9.fc44.x86_64" is already installed. Package "desktop-file-utils-0.28-5.fc44.x86_64" is already installed. Package "fdupes-1:2.4.0-3.fc44.x86_64" is already installed. Package "freeglut-devel-3.8.0-2.fc44.x86_64" is already installed. Package "freetype-devel-2.14.1-2.fc44.x86_64" is already installed. Package "gcc-16.0.1-0.7.fc45.x86_64" is already installed. Package "gcc-c++-16.0.1-0.7.fc45.x86_64" is already installed. Package "glew-devel-2.2.0-12.fc44.x86_64" is already installed. Package "glm-devel-1.0.1-6.fc44.noarch" is already installed. Package "mesa-libGL-devel-26.0.0~rc3-1.fc45.x86_64" is already installed. Package "libappstream-glib-0.8.3-5.fc44.x86_64" is already installed. Package "libpng-devel-2:1.6.53-2.fc44.x86_64" is already installed. Package "libxml2-devel-2.12.10-6.fc44.x86_64" is already installed. Package "mmtf-cpp-devel-1.1.0-9.fc44.x86_64" is already installed. Package "msgpack-devel-3.1.0-23.fc44.x86_64" is already installed. Package "netcdf-devel-4.9.3-2.fc44.x86_64" is already installed. Package "pyproject-rpm-macros-1.18.6-2.fc44.noarch" is already installed. Package "python3-devel-3.14.3-1.fc45.x86_64" is already installed. Package "python3-pillow-12.1.1-1.fc45.x86_64" is already installed. Package "python3-pyside6-devel-6.10.2-1.fc45.x86_64" is already installed. Package "python3-pytest-8.4.2-2.fc44.noarch" is already installed. Package "python3-qt5-devel-5.15.12-0.2.fc44.x86_64" is already installed. Package "python3-packaging-25.0-8.fc44.noarch" is already installed. Package Arch Version Repository Size Installing: python3-numpy x86_64 1:2.4.2-1.fc45 copr_base 41.3 MiB python3-pip noarch 0:26.0.1-1.fc45 copr_base 11.4 MiB python3-setuptools noarch 0:80.10.2-1.fc44 fedora 7.5 MiB Installing dependencies: flexiblas x86_64 0:3.5.0-2.fc44 fedora 38.0 KiB flexiblas-netlib x86_64 0:3.5.0-2.fc44 fedora 16.3 MiB flexiblas-openblas-openmp x86_64 0:3.5.0-2.fc44 fedora 39.1 KiB openblas x86_64 0:0.3.29-2.fc43 fedora 111.7 KiB openblas-openmp x86_64 0:0.3.29-2.fc43 fedora 43.7 MiB python3-numpy-f2py x86_64 1:2.4.2-1.fc45 copr_base 2.1 MiB Transaction Summary: Installing: 9 packages Total size of inbound packages is 23 MiB. Need to download 18 MiB. After this operation, 123 MiB extra will be used (install 123 MiB, remove 0 B). [1/9] python3-setuptools-0:80.10.2-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/9] python3-pip-0:26.0.1-1.fc45.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/9] python3-numpy-f2py-1:2.4.2-1.fc45 100% | 34.9 MiB/s | 465.2 KiB | 00m00s [4/9] flexiblas-0:3.5.0-2.fc44.x86_64 100% | 1.9 MiB/s | 23.1 KiB | 00m00s [5/9] flexiblas-netlib-0:3.5.0-2.fc44.x 100% | 112.3 MiB/s | 4.5 MiB | 00m00s [6/9] flexiblas-openblas-openmp-0:3.5.0 100% | 1.1 MiB/s | 17.2 KiB | 00m00s [7/9] openblas-0:0.3.29-2.fc43.x86_64 100% | 4.6 MiB/s | 42.3 KiB | 00m00s [8/9] openblas-openmp-0:0.3.29-2.fc43.x 100% | 282.1 MiB/s | 5.4 MiB | 00m00s [9/9] python3-numpy-1:2.4.2-1.fc45.x86_ 100% | 114.2 MiB/s | 8.0 MiB | 00m00s -------------------------------------------------------------------------------- [9/9] Total 100% | 245.1 MiB/s | 18.4 MiB | 00m00s Running transaction [ 1/11] Verify package files 100% | 98.0 B/s | 9.0 B | 00m00s [ 2/11] Prepare transaction 100% | 87.0 B/s | 9.0 B | 00m00s [ 3/11] Installing openblas-0:0.3.29-2. 100% | 110.8 MiB/s | 113.5 KiB | 00m00s [ 4/11] Installing openblas-openmp-0:0. 100% | 560.1 MiB/s | 43.7 MiB | 00m00s [ 5/11] Installing flexiblas-netlib-0:3 100% | 308.1 MiB/s | 16.3 MiB | 00m00s [ 6/11] Installing flexiblas-0:3.5.0-2. 100% | 38.2 MiB/s | 39.2 KiB | 00m00s [ 7/11] Installing flexiblas-openblas-o 100% | 13.0 MiB/s | 39.9 KiB | 00m00s [ 8/11] Installing python3-numpy-1:2.4. 100% | 315.3 MiB/s | 41.6 MiB | 00m00s [ 9/11] Installing python3-numpy-f2py-1 100% | 83.8 MiB/s | 2.2 MiB | 00m00s [10/11] Installing python3-pip-0:26.0.1 100% | 170.0 MiB/s | 11.7 MiB | 00m00s [11/11] Installing python3-setuptools-0 100% | 89.0 MiB/s | 7.7 MiB | 00m00s Warning: skipped OpenPGP checks for 3 packages from repository: copr_base Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.o3H1QP + 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/.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/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + 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/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.4.2) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 80.10.2) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.4.2) Handling pillow==10.3.0 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pillow==10.3.0 Handling pytest==8.2.2 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pytest==8.2.2 + cat /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: Copr repository 100% | 11.7 KiB/s | 1.5 KiB | 00m00s fedora 100% | 101.2 KiB/s | 23.0 KiB | 00m00s Repositories loaded. Nothing to do. Package "catch2-devel-2.13.10-9.fc44.x86_64" is already installed. Package "desktop-file-utils-0.28-5.fc44.x86_64" is already installed. Package "fdupes-1:2.4.0-3.fc44.x86_64" is already installed. Package "freeglut-devel-3.8.0-2.fc44.x86_64" is already installed. Package "freetype-devel-2.14.1-2.fc44.x86_64" is already installed. Package "gcc-16.0.1-0.7.fc45.x86_64" is already installed. Package "gcc-c++-16.0.1-0.7.fc45.x86_64" is already installed. Package "glew-devel-2.2.0-12.fc44.x86_64" is already installed. Package "glm-devel-1.0.1-6.fc44.noarch" is already installed. Package "mesa-libGL-devel-26.0.0~rc3-1.fc45.x86_64" is already installed. Package "libappstream-glib-0.8.3-5.fc44.x86_64" is already installed. Package "libpng-devel-2:1.6.53-2.fc44.x86_64" is already installed. Package "libxml2-devel-2.12.10-6.fc44.x86_64" is already installed. Package "mmtf-cpp-devel-1.1.0-9.fc44.x86_64" is already installed. Package "msgpack-devel-3.1.0-23.fc44.x86_64" is already installed. Package "netcdf-devel-4.9.3-2.fc44.x86_64" is already installed. Package "pyproject-rpm-macros-1.18.6-2.fc44.noarch" is already installed. Package "python3-devel-3.14.3-1.fc45.x86_64" is already installed. Package "python3-pillow-12.1.1-1.fc45.x86_64" is already installed. Package "python3-pyside6-devel-6.10.2-1.fc45.x86_64" is already installed. Package "python3-pytest-8.4.2-2.fc44.noarch" is already installed. Package "python3-qt5-devel-5.15.12-0.2.fc44.x86_64" is already installed. Package "python3-packaging-25.0-8.fc44.noarch" is already installed. Package "python3-pip-26.0.1-1.fc45.noarch" is already installed. Package "python3-setuptools-80.10.2-1.fc44.noarch" is already installed. Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1768608000 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.d8zoXI + 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/.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/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + 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/pyproject-wheeldir --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-buildrequires -p Handling numpy>=1.26.4,<3 from build-system.requires Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.4.2) Handling setuptools>=69.2.0 from build-system.requires Requirement satisfied: setuptools>=69.2.0 (installed: setuptools 80.10.2) Handling numpy>=1.26.4,<3 from pyproject.toml generated metadata: [dependencies] (pymol) Requirement satisfied: numpy>=1.26.4,<3 (installed: numpy 2.4.2) Handling pillow==10.3.0 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pillow==10.3.0 Handling pytest==8.2.2 from pyproject.toml generated metadata: [optional-dependencies] test (pymol) Ignoring alien requirement: pytest==8.2.2 + cat /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.wOFPct + 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/.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/.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/pyproject-wheeldir Processing ./. Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) /usr/lib/python3.14/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 2027-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-314/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/python3.14/site-packages/numpy/_core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.14;/usr/include/python3.14; -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-314-x86_64-linux-gnu.so -- The C compiler identification is GNU 16.0.1 -- The CXX compiler identification is GNU 16.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.5s) -- 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-314/_cmd cmake --build . --config Release -j4 /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-314/_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-314/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_cmd' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_cmd/CMakeFiles/_cmd.dir/DependInfo.cmake "--color=" _cmd gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_cmd' [ 0%] Building CXX object CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o [ 0%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c.o [ 0%] Building CXX object CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o [ 1%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/mmtf-c/mmtf_parser.cpp.o -MF CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o.d -o CMakeFiles/_cmd.dir/contrib/mmtf-c/mmtf_parser.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c/mmtf_parser.cpp /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/build/generated/ShaderText.cpp.o -MF CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o.d -o CMakeFiles/_cmd.dir/build/generated/ShaderText.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated/ShaderText.cpp /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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:1497:10: warning: variable ‘bc’ set but not used [-Wunused-but-set-variable=] 1497 | int i, bc = 0; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘DEN_read_volumetric_data’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 970 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 971 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘POT_read_volumetric_data’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1113 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1114 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘abinit_header’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1511 | fread(skip, 1, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘GEO_read_next_timestep’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 619 | fscanf(data->file, "%*s %f %f %f", &x, &y, &z); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 2%] Building 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function ‘print_input_data’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:319:7: warning: variable ‘shellcount’ set but not used [-Wunused-but-set-variable=] 319 | int shellcount=0; | ^~~~~~~~~~ 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: 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: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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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*) [clone .part.0]’: /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 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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:974, 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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] ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 ‘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 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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: In function ‘fio_fread’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:413:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=] 413 | fio_size_t len = 0; | ^~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function ‘fio_fwrite’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:532:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=] 532 | fio_size_t len = 0; | ^~~ /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) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 609 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 605 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘open_ccp4_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:279:3: warning: ‘dataOffset’ may be used uninitialized [-Wmaybe-uninitialized] 279 | if (dataOffset != (CCP4HDSIZE + symBytes)) { | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:89:8: note: ‘dataOffset’ was declared here 89 | long dataOffset, filesize; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/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) | ^~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/cubeplugin.cpp: In function ‘open_cube_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:179:10: warning: ‘__strncat_chk’ output may be truncated copying 240 bytes from a string of length 1023 [-Wstringop-truncation] 179 | strncat(voltmpl.dataname, readbuf, 240); // 240 is max space left after | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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; | ^~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘print_input_data’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1005:7: warning: variable ‘shellcount’ set but not used [-Wunused-but-set-variable=] 1005 | int shellcount=0; | ^~~~~~~~~~ /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]) { | ^~~~~~~~~~~~~ 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) { | ^~~~~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/graspplugin.cpp: In function ‘void line3(FILE*, GRASSP*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 186 | fread(line3, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:3: note: in expansion of macro ‘TRASH’ 284 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 285 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:3: note: in expansion of macro ‘TRASH’ 291 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:3: note: in expansion of macro ‘TRASH’ 305 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:3: note: in expansion of macro ‘TRASH’ 307 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:3: note: in expansion of macro ‘TRASH’ 311 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:3: note: in expansion of macro ‘TRASH’ 313 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:3: note: in expansion of macro ‘TRASH’ 318 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 319 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:3: note: in expansion of macro ‘TRASH’ 320 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:3: note: in expansion of macro ‘TRASH’ 328 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 329 | fread(line, 1, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:3: note: in expansion of macro ‘TRASH’ 330 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:3: note: in expansion of macro ‘TRASH’ 354 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(vertex, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:3: note: in expansion of macro ‘TRASH’ 356 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:3: note: in expansion of macro ‘TRASH’ 357 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(access, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:3: note: in expansion of macro ‘TRASH’ 359 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:3: note: in expansion of macro ‘TRASH’ 360 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 361 | fread(normal, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:3: note: in expansion of macro ‘TRASH’ 362 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:5: note: in expansion of macro ‘TRASH’ 371 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 372 | fread(triangle, 3 * sizeof(int), ntriangles, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:5: note: in expansion of macro ‘TRASH’ 373 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:5: note: in expansion of macro ‘TRASH’ 374 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 375 | fread(properties, 3 * sizeof(float), nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:5: note: in expansion of macro ‘TRASH’ 394 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 395 | fread(striangle, sizeof(short), 3 * ntriangles, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:5: note: in expansion of macro ‘TRASH’ 396 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | #define TRASH fread(trash, 4, 1, infile) | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:5: note: in expansion of macro ‘TRASH’ 397 | TRASH; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 398 | fread(properties, sizeof(float), 3 * nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_coordinates’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] 1618 | strncpy(atm->type, atname, sizeof(atm->type)); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /usr/include/string.h:580, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:155: In function ‘strncpy’, inlined from ‘get_basis_options’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1431:5: /usr/include/bits/string_fortified.h:112:10: warning: ‘strncpy’ accessing 8192 bytes at offsets 50 and 40 may overlap up to 8142 bytes at offset [50, 8191] [-Wrestrict] 112 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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) { | ^~~~~~~~~~~~~~~ /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)); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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)); | ^ 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/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)); | ^ [ 10%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/hash.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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:79: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function ‘fio_fread’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:413:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=] 413 | fio_size_t len = 0; | ^~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function ‘fio_fwrite’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:532:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=] 532 | fio_size_t len = 0; | ^~~ /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); | ^ 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: 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:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘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); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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:974, 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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /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; | ^~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/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/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/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/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/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/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/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/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 | ~~~~~^~~~~~~~~~~~~~~~~~~~ /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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); | ~~~~~^~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘read_next_timestep’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable ‘numatoms’ set but not used [-Wunused-but-set-variable=] 103 | int i, numatoms; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘open_namdbin_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:78:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fread(&filen, sizeof(namdbin_int32), 1, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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); | ~~~~~~^~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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); | ^ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp: In function ‘int read_pbeq_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/pbeqplugin.cpp:255:7: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 255 | int count=0; | ^~~~~ 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: 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) { | ^~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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) | ^~~~~~~~~~~ /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(), | ^ 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); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/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:500:7: warning: variable ‘chargecount’ set but not used [-Wunused-but-set-variable=] 500 | int chargecount = 0; | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:501:7: warning: variable ‘occupancycount’ set but not used [-Wunused-but-set-variable=] 501 | int occupancycount = 0; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:502:7: warning: variable ‘bfactorcount’ set but not used [-Wunused-but-set-variable=] 502 | int bfactorcount = 0; | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable ‘oldChain’ [-Wunused-variable] 503 | char oldChain[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readAngleBonds(molfile_atom_t*, pdbxParser*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable ‘bondTable’ [-Wunused-variable] 803 | int bondTable[32]; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable ‘j’ [-Wunused-variable] 807 | int i, pos, j, k; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable ‘modelNum’ [-Wunused-variable] 811 | char modelNum[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable ‘atom’ [-Wunused-variable] 822 | molfile_atom_t * atom; | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable ‘test’ [-Wunused-variable] 884 | int test = parser->nbonds + bnum; | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readRMSDBonds(molfile_atom_t*, pdbxParser*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable ‘bondTable’ [-Wunused-variable] 984 | int bondTable[32]; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable ‘j’ [-Wunused-variable] 988 | int i, pos, j, k; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable ‘modelNum’ [-Wunused-variable] 991 | char modelNum[8]; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable ‘atom’ [-Wunused-variable] 1002 | molfile_atom_t * atom; | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘void* open_file_write(const char*, const char*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable ‘fd’ [-Wunused-variable] 1409 | FILE* fd; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:313:14: warning: ‘float stringToFloat(char*)’ defined but not used [-Wunused-function] 313 | static float stringToFloat(char * str) { | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘const char* get_pte_label(int)’ defined but not used [-Wunused-function] 95 | static const char *get_pte_label(const int idx) | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function ‘open_pdb_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] 190 | strncpy(date, record + 50, 9); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] 200 | strncpy(pdbcode, record + 62, 4); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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:784:16: warning: ‘strncpy’ specified bound 32 equals destination size [-Wstringop-truncation] /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] /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/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); | ^ /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:784:16: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] /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] /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:786:16: warning: ‘strncpy’ specified bound 8 equals destination size [-Wstringop-truncation] 786 | strncpy(arr, value.c_str(), N); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘int read_plt_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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:784:16: warning: ‘strncpy’ specified bound 16 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:784:16: warning: ‘strncpy’ specified bound 16 equals destination size [-Wstringop-truncation] /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 16 equals destination size [-Wstringop-truncation] /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 16 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:886:16: warning: ‘strncpy’ specified bound 16 equals destination size [-Wstringop-truncation] 886 | strncpy( a.name, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘void* open_plt_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fread(intHeader, sizeof(int), 5, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fread(floatHeader, sizeof(float), 6, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 18%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/pqrplugin.c: In function ‘read_pqr_timestep’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:109:3: warning: ‘strncpy’ output may be truncated copying 80 bytes from a string of length 81 [-Wstringop-truncation] 109 | strncpy(tmp, record, PQR_RECORD_LENGTH); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘read_pqr_structure’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:137:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 68 [-Wstringop-truncation] 137 | strncpy(name, record+12, 4); name[4] = 0; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:138:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 63 [-Wstringop-truncation] 138 | strncpy(resname, record+17, 4); resname[4] = 0; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:139:3: warning: ‘strncpy’ output may be truncated copying 1 byte from a string of length 59 [-Wstringop-truncation] 139 | strncpy(chain, record+21, 1); chain[1] = 0; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:140:3: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 58 [-Wstringop-truncation] 140 | strncpy(resid, record+22, 4); resid[4] = 0; | ^ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: ‘fortread_4’ defined but not used [-Wunused-function] 103 | static int fortread_4(void *dest, int n, int swap, FILE *fd) { | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘fort_get_endian_reclen’ defined but not used [-Wunused-function] 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘fort_eat_recmark’ defined but not used [-Wunused-function] 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘swap8_aligned’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1629 | fread (&len, sizeof(int), 1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1631 | fread (str, len, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void get_binary_item(FILE*, int, int*, unsigned int*, double*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2057 | fread (ptr, 1, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2063 | fread (ptr, 1, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2069 | fread (ptr, 2, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2075 | fread (ptr, 2, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2081 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2087 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2093 | fread (ptr, 4, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2099 | fread (ptr, 8, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:27: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] 110 | static void swap4_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] 46 | static void swap4_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 ‘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; | ^~~~~~~~~~ /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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)); | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_timestep’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 224 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_structure’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 174 | for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 180 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 194 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘open_vasp5xdatcar_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 77 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fread(&headersize, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 124 | static void swap8_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] 65 | static void swap8_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ [ 22%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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’: [ 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: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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 ‘read_vaspchgcar_metadata’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘open_vaspchgcar_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_data’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 238 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_metadata’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘open_vaspparchg_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c.o [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function ‘vtf_read_bonds’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:147:48: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 147 | sprintf(message, "vtfplugin:%d: error: %s: \"%s\"\n", | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_timestep(void*, int, molfile_timestep_t*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 288 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 365 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 387 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 395 | fgets(nextline, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 455 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_structure(void*, int*, molfile_atom_t*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 250 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘void* open_xbgf_read(const char*, const char*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function ‘vtf_open_file_read’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:538:9: warning: ‘__strncat_chk’ output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] 538 | strncat(msg, keyword, 200); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:629:7: warning: ‘__strncat_chk’ output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] 629 | strncat(msg, keyword, 200); | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:276:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable=] 276 | int x, y, z, xsize, ysize, zsize, xysize, total; | ^~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data_ex(void*, molfile_volumetric_readwrite_t*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:338:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable=] 338 | int x, y, z, xsize, ysize, zsize, xysize, total; | ^~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/vtkplugin.cpp: In function ‘open_vtk_read(char const*, char const*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:152:10: warning: ‘strncpy’ output may be truncated copying 256 bytes from a string of length 2039 [-Wstringop-truncation] 152 | strncpy(vtk->title, inbuf, sizeof(vtk->title) - 1); | ^ [ 26%] Building C object CMakeFiles/_cmd.dir/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c.o /usr/bin/gcc -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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*) [clone .part.0]’: /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); | ^ [ 26%] Building CXX object CMakeFiles/_cmd.dir/layer0/Bezier.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 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/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/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/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 ‘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/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)); | ^ [ 27%] Building CXX object CMakeFiles/_cmd.dir/layer0/Block.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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-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 /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); | ^ /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*) [clone .part.0]’: /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)); | ^ [ 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 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-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -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/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 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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/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: 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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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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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-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/MemoryUsage.cpp: In function ‘size_t pymol::memory_usage()’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp:38:21: warning: use of assignment suppression and length modifier together in gnu_scanf format [-Wformat=] 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryUsage.cpp:38:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object CMakeFiles/_cmd.dir/layer0/Parse.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 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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/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 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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/Pixmap.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Pixmap.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Pixmap.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/PostProcess.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include 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-I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 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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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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 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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/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 [ 36%] Building CXX object CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/Sphere.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Sphere.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Sphere.cpp 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, | ^~~~~~~~~~ [ 37%] Building CXX object CMakeFiles/_cmd.dir/layer0/TTT.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 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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/TTT.cpp.o -MF CMakeFiles/_cmd.dir/layer0/TTT.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/TTT.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/TTT.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderPrg.cpp:20: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 37%] Building CXX object CMakeFiles/_cmd.dir/layer0/Tetsurf.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src 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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/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 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 38%] Building CXX object CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/Tracker.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Tracker.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Tracker.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Tetsurf.cpp: In function ‘int TetsurfFindActiveBoxes(CTetsurf*, cIsosurfaceMode, int&, int, pymol::vla&, pymol::vla&, const CarveHelper*, cIsosurfaceSide)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Tetsurf.cpp:775:7: warning: variable ‘n_active’ set but not used [-Wunused-but-set-variable=] 775 | int n_active = 0; | ^~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:36, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Texture.cpp:34: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Texture.cpp: In function ‘bool TextureIsCharTextured(PyMOLGlobals*, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Texture.cpp:130:9: warning: unused variable ‘use_shader’ [-Wunused-variable] 130 | short use_shader = (short) SettingGetGlobal_b(G, cSetting_use_shaders); | ^~~~~~~~~~ [ 38%] Building CXX object CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 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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/Triangle.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Triangle.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Triangle.cpp [ 39%] Building CXX object CMakeFiles/_cmd.dir/layer0/Util.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c 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/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Util.cpp /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Triangle.cpp: In function ‘int* TriangleMakeStripVLA(TriangleSurfaceRec*, float*, float*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Triangle.cpp:116:13: warning: variable ‘cc’ set but not used [-Wunused-but-set-variable=] 116 | int c, a, cc = 0; | ^~ [ 39%] Building CXX object CMakeFiles/_cmd.dir/layer0/Util2.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-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/Util2.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Util2.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Util2.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Util2.cpp [ 39%] Building CXX object CMakeFiles/_cmd.dir/layer0/Vector.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/Vector.cpp.o -MF CMakeFiles/_cmd.dir/layer0/Vector.cpp.o.d -o CMakeFiles/_cmd.dir/layer0/Vector.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Vector.cpp [ 40%] Building CXX object CMakeFiles/_cmd.dir/layer0/Word.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 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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/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 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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/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 [ 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 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/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/marching_cubes.cpp [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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; | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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: /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; | ~~~^~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 ‘int OptimizePointsToVBO(const CGO*, CGO*, int, float*, float*, short int*, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:2237:35: warning: variable ‘vpl’ set but not used [-Wunused-but-set-variable=] 2237 | int pl = 0, plc = 0, idxpl = 0, vpl = 0, nxtn; | ^~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘bool CGOProcessCGOtoArrays(const CGO*, CGO*, CGO*, float*, float*, int*, float*, float*, uchar*, float*, uchar*, float*, float*, bool&, bool&, bool&)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:2466:24: warning: variable ‘vpl’ set but not used [-Wunused-but-set-variable=] 2466 | int pl = 0, plc = 0, vpl = 0; | ^~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘bool CGOProcessScreenCGOtoArrays(PyMOLGlobals*, CGO*, float*, float*, float*, uchar*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:2706:11: warning: variable ‘nverts’ set but not used [-Wunused-but-set-variable=] 2706 | int nverts = 0, ipl = 0; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘bool OptimizeLinesToVBONotIndexed(const CGO*, CGO*, const CGOCount&, float*, float*, short int*, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:2990:35: warning: variable ‘vpl’ set but not used [-Wunused-but-set-variable=] 2990 | int pl = 0, plc = 0, idxpl = 0, vpl = 0, nxtn; | ^~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp: In function ‘CGO* CGOConvertLinesToShaderCylinders(const CGO*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:7074:7: warning: variable ‘tot_nverts’ set but not used [-Wunused-but-set-variable=] 7074 | int tot_nverts = 0, tot_ncyls = 0; | ^~~~~~~~~~ /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) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGO.cpp:8978:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable=] 8978 | int ok = true; | ^~ 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, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGOGL.cpp: In function ‘void CGORenderGLAlpha(CGO*, RenderInfo*, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/CGOGL.cpp:2487:24: warning: variable ‘ntris’ set but not used [-Wunused-but-set-variable=] 2487 | int delta = 1, ntris = 0; | ^~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 45%] Building CXX object CMakeFiles/_cmd.dir/layer1/Extrude.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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())) { | ~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Control.cpp:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /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]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp:302:35: 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]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp:624:38: 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]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp:739:42: 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]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Color.cpp:741:54: 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) { | ~~^~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:22: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Control.cpp: In function ‘void ControlFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CControl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Control.cpp:410:3: note: in expansion of macro ‘DeleteP’ 410 | DeleteP(G->Control); | ^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp: In function ‘ExtrudeComputeTangents(CExtrude*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Extrude.cpp:742:13: warning: ‘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++); | ^~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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:949:37: warning: ‘start’ 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:876:7: note: ‘start’ was declared here 876 | int start, stop; | ^~~~~ /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; | ^~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 46%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/FontGLUT8x13.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUT8x13.cpp.o -c 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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/FontGLUTHel10.cpp.o -MF CMakeFiles/_cmd.dir/layer1/FontGLUTHel10.cpp.o.d -o CMakeFiles/_cmd.dir/layer1/FontGLUTHel10.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUTHel10.cpp [ 47%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUTHel12.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/FontGLUTHel12.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/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, | ^~~~~~~~~~ [ 48%] Building CXX object CMakeFiles/_cmd.dir/layer1/FontGLUTHel18.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 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-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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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); | ^~~~~~~~~~~ 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/Ortho.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp:1783:13: warning: ‘void OrthoDrawFontTextureDebug(PyMOLGlobals*, CGO*)’ defined but not used [-Wunused-function] 1783 | static void OrthoDrawFontTextureDebug(PyMOLGlobals* G, CGO* orthoCGO) | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ortho.cpp:775:13: warning: ‘void OrthoKeyCmmd(PyMOLGlobals*, unsigned char)’ defined but not used [-Wunused-function] 775 | static void OrthoKeyCmmd(PyMOLGlobals* G, unsigned char k) | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp: In function ‘PLabelAtomAlt(PyMOLGlobals*, AtomInfoType*, char const*, char const*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.cpp:323:12: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 323 | strncpy(label, origexpr, OrthoLineLength); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:580, from /usr/include/python3.14/Python.h:40, 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:152:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 152 | 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:152:33: warning: ‘__strcat_chk’ accessing 4611686018427387981 or more bytes at offsets [76, 261196] and [-4611686018427387904, 4611686018427387903] may overlap 1 byte at offset [76, 9223372036854775807] [-Wrestrict] 152 | return __builtin___strcat_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 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-I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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++) { | ~~^~~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/_cmd.dir/layer1/Picking.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP 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-D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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++/16/bits/stl_uninitialized.h:63, from /usr/include/c++/16/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++/16/bits/stl_algobase.h:257:5: note: declared here 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ [ 52%] Building CXX object CMakeFiles/_cmd.dir/layer1/Scene.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 ‘ov_size idtf_dump_model_nodes(char**, ov_size, IdtfResourceMesh*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:1863:21: warning: variable ‘mesh’ set but not used [-Wunused-but-set-variable=] 1863 | IdtfResourceMesh *mesh = mesh_vla; | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp: In function ‘void RayRender(CRay*, unsigned int*, double, float, int, unsigned int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6070:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6070 | if(x_stop > width) | ~~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6072:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6072 | if(y_stop > height) | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6153:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6153 | for(y = 0; y < height; y++) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6154:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6154 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6165:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6165 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6176:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6176 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6237:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6237 | for(y = 0; y < height; y++) | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6238:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6238 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6248:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6248 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6260:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6260 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6311:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6311 | for(y = 0; y < height; y++){ | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6331:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6331 | for(x = 0; x < width; x++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6350:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6350 | if(x < (width - 1)) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6364:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6364 | if(y < (height - 1)) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6378:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6378 | if(x && (y < (height - 1))) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6385:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6385 | if(y && (x < (width - 1))) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6392:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6392 | if((y < (height - 1)) && (x < (width - 1))) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6392:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6392 | if((y < (height - 1)) && (x < (width - 1))) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6548:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6548 | for(y = 0; y < height; y++) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Ray.cpp:6549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6549 | for(x = 0; x < width; x++) { | ~~^~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Rep.cpp:30: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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 lambda function: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4122:36: warning: implicit capture of ‘this’ via ‘[=]’ is deprecated in C++20 [-Wdeprecated] 4122 | std::function deferred = [=]() { | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4122:36: note: add explicit ‘this’ or ‘*this’ capture /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4139:36: warning: implicit capture of ‘this’ via ‘[=]’ is deprecated in C++20 [-Wdeprecated] 4139 | std::function deferred = [=]() { | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4139:36: note: add explicit ‘this’ or ‘*this’ capture /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4166:3: warning: deleting object of polymorphic class type ‘CScene’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 4166 | delete G->Scene; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘void SceneObjectUpdateSpawn(PyMOLGlobals*, CObjectUpdateThreadInfo*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4614:12: warning: variable ‘n’ set but not used [-Wunused-but-set-variable=] 4614 | int a, n = 0; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp: In function ‘void SceneUpdate(PyMOLGlobals*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.cpp:4696:15: warning: variable ‘n_obj’ set but not used [-Wunused-but-set-variable=] 4696 | int n_obj = 0; | ^~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 function ‘SceneRenderPickingMultiPick(PyMOLGlobals*, SceneUnitContext*, Multipick*, unsigned int)’, inlined from ‘SceneRenderPicking(PyMOLGlobals*, int, ClickSide, int, Picking*, int, int, Multipick*, SceneUnitContext*, unsigned int)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:323:32: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:257:7: warning: ‘previous.src.index’ may be used uninitialized [-Wmaybe-uninitialized] 257 | if (pik->src.index != previous.src.index || | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp: In function ‘SceneRenderPicking(PyMOLGlobals*, int, ClickSide, int, Picking*, int, int, Multipick*, SceneUnitContext*, unsigned int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/ScenePicking.cpp:246:11: note: ‘previous.src.index’ was declared here 246 | Picking previous; | ^~~~~~~~ [ 54%] Building CXX object CMakeFiles/_cmd.dir/layer1/SceneRay.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, from /usr/include/c++/16/bits/locale_classes.h:43, from /usr/include/c++/16/bits/ios_base.h:43, from /usr/include/c++/16/ios:46, from /usr/include/c++/16/bits/ostream.h:43, from /usr/include/c++/16/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 ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/SceneRay.cpp:2: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/_cmd.dir/layer1/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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, | ^~~~~~~~~~ /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 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 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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/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 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ /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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, 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 ()); | ~~~~~~~~~~~~~~~~~ /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); | ^~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingUniqueResetAll(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp:501:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 501 | for (int a = 2; a < I->entry.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp:2020:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2020 | if (SettingGetGlobal_b(G, cSetting_precomputed_lighting)) | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Setting.cpp:2022:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022 | SceneInvalidate(G); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp: At global scope: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Seq.cpp:717:13: warning: ‘void SeqPurgeRowVLA(PyMOLGlobals*)’ defined but not used [-Wunused-function] 717 | static void SeqPurgeRowVLA(PyMOLGlobals * G) | ^~~~~~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/_cmd.dir/layer1/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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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-Wp,-D_GLIBCXX_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 [ 58%] Building CXX object CMakeFiles/_cmd.dir/layer1/TypeFace.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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-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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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, | ^~~~~~~~~~ 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); | ^~~~~~~ [ 59%] Building CXX 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-I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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; | 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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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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, | ^~~~~~~~~~ /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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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] [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘PyObject* ObjectCGOAllStatesAsPyList(ObjectCGO*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:54:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘int ObjectCGOAllStatesFromPyList(ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:105:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 105 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:206:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 206 | if((state >= 0) && (state < I->State.size())) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:503:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 503 | if (!ray) | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:505:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 505 | ObjectCGORenderState(G, pass, ray, I, info, sobj, color, ramp, use_shader, cgo_lighting); | ^~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:24: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h: In copy constructor ‘ObjectCGOState::ObjectCGOState(const ObjectCGOState&)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h:28:17: warning: ‘ObjectCGOState::G’ will be initialized after [-Wreorder] 28 | PyMOLGlobals* G; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h:27:25: warning: ‘pymol::cache_ptr ObjectCGOState::renderCGO’ [-Wreorder] 27 | pymol::cache_ptr renderCGO; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:532:1: warning: when initialized here [-Wreorder] 532 | ObjectCGOState::ObjectCGOState(const ObjectCGOState& other) | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h:29:58: warning: ‘ObjectCGOState::hasOpaque’ will be initialized after [-Wreorder] 29 | bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.h:29:44: warning: ‘bool ObjectCGOState::cgo_lighting’ [-Wreorder] 29 | bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque; | ^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:532:1: warning: when initialized here [-Wreorder] 532 | ObjectCGOState::ObjectCGOState(const ObjectCGOState& other) | ^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromCGO(PyMOLGlobals*, ObjectCGO*, CGO*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:617:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 617 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGODefine(PyMOLGlobals*, ObjectCGO*, PyObject*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:682:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 682 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:665:7: warning: variable ‘size_n’ set but not used [-Wunused-but-set-variable=] 665 | int size_n; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromFloatArray(PyMOLGlobals*, ObjectCGO*, float*, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCGO.cpp:740:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 740 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectCallback.cpp:28: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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: 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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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, | ^~~~~~~~~~ /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++) | ~~^~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectGadgetRamp.cpp:28: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 68%] Building CXX object CMakeFiles/_cmd.dir/layer2/ObjectMesh.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 ‘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) { | ~~~~~~~~~~~~~~~~^~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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, | ^~~~~~~~~~ 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 function ‘void ObjMolCoordSetUpdateSpawn(PyMOLGlobals*, CCoordSetUpdateThreadInfo*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.cpp:10524:12: warning: variable ‘n’ set but not used [-Wunused-but-set-variable=] 10524 | int a, n = 0; | ^ /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) { | ~~^~~~~~~ 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/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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, from /usr/include/c++/16/bits/locale_classes.h:43, from /usr/include/c++/16/bits/ios_base.h:43, from /usr/include/c++/16/ios:46, from /usr/include/c++/16/bits/ostream.h:43, from /usr/include/c++/16/bits/unique_ptr.h:42, from /usr/include/c++/16/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/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 ()); | ~~~~~~~~~~~~~~~~~ /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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘std::vector ObjectMoleculeGetMolMappingVec(const ObjectMolecule&)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp:42:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 42 | for (size_t b = 0; b < objmol.NBond; ++b) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp: In function ‘void ObjectMoleculePBCUnwrap(ObjectMolecule&, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule3.cpp:151:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 151 | for (unsigned atm = 0; atm != objmol.NAtom; ++atm) { | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, from /usr/include/c++/16/bits/locale_classes.h:43, from /usr/include/c++/16/bits/ios_base.h:43, from /usr/include/c++/16/ios:46, from /usr/include/c++/16/bits/ostream.h:43, from /usr/include/c++/16/bits/unique_ptr.h:42, from /usr/include/c++/16/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/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 ()); | ~~~~~~~~~~~~~~~~~ /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/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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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 file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:33: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘PyObject* ObjectSliceAllStatesAsPyList(ObjectSlice*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:78:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 78 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:210:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for(a = 0; a < State.size(); a++) { | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:633:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 633 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceDrag(ObjectSlice*, int, int, float*, float*, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:679:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 679 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘int ObjectSliceGetVertex(ObjectSlice*, int, int, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:750:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 750 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:925:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 925 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:967:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 967 | if(cur_state >= I->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:981:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 981 | if(state < I->State.size()) | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1226 | if(cur_state >= I->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSliceState* ObjectSliceStateGetActive(ObjectSlice*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1244:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1244 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘ObjectSlice* ObjectSliceFromMap(PyMOLGlobals*, ObjectSlice*, ObjectMap*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1285:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1285 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp: In function ‘void ObjectSliceRecomputeExtent(ObjectSlice*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSlice.cpp:1362:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1362 | for(a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:35: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:84:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 84 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:237:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | if(state < I->State.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::invalidate(cRep_t, cRepInv_t, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:282:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 282 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceInvalidateMapName(ObjectSurface*, const char*, const char*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:312:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 312 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘ObjectSurface* ObjectSurfaceFromBox(PyMOLGlobals*, ObjectSurface*, ObjectMap*, int, int, float*, float*, float, cIsosurfaceMode, float, pymol::vla&&, cIsosurfaceSide, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:1042:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1042 | if(I->State.size() <= state) { | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectSurface.cpp:1138:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1138 | for(int a = 0; a < I->State.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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/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 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); | ^~ 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 between 30 and 285 bytes into a destination of size 255 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/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); | ^~ /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, | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, from /usr/include/c++/16/bits/locale_classes.h:43, from /usr/include/c++/16/bits/ios_base.h:43, from /usr/include/c++/16/ios:46, from /usr/include/c++/16/bits/ostream.h:43, from /usr/include/c++/16/bits/unique_ptr.h:42, from /usr/include/c++/16/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/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 ()); | ~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp: In function ‘int GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals*, ObjectMolecule*, CoordSet*, CGO*, CExtrude*, int, int*, float*, float*, float*, const CCInOut*, int*, float*, int, int, float, float)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1591:19: warning: variable ‘v2’ set but not used [-Wunused-but-set-variable=] 1591 | float *v, *v1, *v2, *vo, *d; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1591:24: warning: variable ‘vo’ set but not used [-Wunused-but-set-variable=] 1591 | float *v, *v1, *v2, *vo, *d; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCartoon.cpp:1591:29: warning: variable ‘d’ set but not used [-Wunused-but-set-variable=] 1591 | float *v, *v1, *v2, *vo, *d; | ^ /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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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/RepCylBond.cpp: In member function ‘virtual void RepCylBond::render(RenderInfo*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepCylBond.cpp:174:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable=] 174 | int ok = true; | ^~ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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, | ^~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/CoordSet.h:22, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.h:21, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp:25: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp: In function ‘RepDotDoNew(CoordSet*, cRepDot_t, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp:463:46: warning: ‘vn’ may be used uninitialized [-Wmaybe-uninitialized] 463 | I->VN = ReallocForSure(I->VN, float, (vn - I->VN)); | ~~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepDot.cpp:263:14: note: ‘vn’ was declared here 263 | float *v, *vn; | ^~ [ 74%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepMesh.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 /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, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp: In function ‘Rep* RepNonbondedSphereNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepNonbondedSphere.cpp:145:7: warning: variable ‘NP’ set but not used [-Wunused-but-set-variable=] 145 | int NP = 0; | ^~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 In file included from /usr/include/c++/16/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++/16/bits/unique_ptr.h:397:19: warning: ‘field’ may be used uninitialized [-Wmaybe-uninitialized] 397 | 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; | ^~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 ‘Rep* RepRibbonNew(CoordSet*, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:189:24: warning: variable ‘v3’ set but not used [-Wunused-but-set-variable=] 189 | float *v, *v1, *v2, *v3; | ^~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphere.cpp:34: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphereGenerate.cpp:20: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSphereImmediate.cpp:20: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepRibbon.cpp:422:15: warning: ‘MEM [(float *)_701]’ 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 *)_701 + 8B]’ may be used uninitialized [-Wmaybe-uninitialized] 424 | *(v1++) = *(v++); | ^~~~~~ [ 77%] Building CXX object CMakeFiles/_cmd.dir/layer2/RepSurface.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/SideChainHelper.cpp.o -MF CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o.d -o CMakeFiles/_cmd.dir/layer2/SideChainHelper.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/SideChainHelper.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepWireBond.cpp:26: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:35: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:2690:15: warning: variable ‘natoms’ set but not used [-Wunused-but-set-variable=] 2690 | int natoms = 0, nbits = 0; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp: In function ‘int SurfaceJobRun(PyMOLGlobals*, SurfaceJob*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:3911:27: warning: variable ‘n0’ set but not used [-Wunused-but-set-variable=] 3911 | float *v0, *n0; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4701:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4701 | for (auto j = 0; j < edges[i].size(); j += 3) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4713:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4713 | for (auto j = 0; j < edges[i].size(); j += 3) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/RepSurface.cpp:4724:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4724 | for (auto i = 0; i < unique_edges.size(); i += 2) { | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/AtomIterators.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/CifDataValueFormatter.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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, | ^~~~~~~~~~ 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/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/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals*, pymol::zstring_view, PyObject*, pymol::zstring_view, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:171:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 171 | for(size_t c = 0; c < n_cols; ++c) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/ExecutivePython.cpp:180:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 180 | for(size_t i = 0; i < n_idx; ++i) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSmooth(PyMOLGlobals*, const char*, int, int, int, int, int, int, float, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:6186:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 6186 | for (int c = 0; c < n_atom; ++c) { | ~~^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveMapSet(PyMOLGlobals*, const char*, int, const char*, int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:6356:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 6356 | if(obj->State.size() > max_n_state) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:6467:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6467 | if(src_state < obj->State.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveRenderSelectionsFromTargets(PyMOLGlobals*, bool, int, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:8341:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 8341 | if (I->selIndicatorsCGO = optimized) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘float ExecutiveRMSPairs(PyMOLGlobals*, const std::vector&, int, bool)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:11154:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 11154 | for(a = 0; a < pairs; a++) { | ~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:11159:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 11159 | if(a < (pairs - 1)) | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveColor(PyMOLGlobals*, const char*, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:12528:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable=] 12528 | int ok = false; | ^~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14196:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 14196 | for (unsigned idx = 0; idx < cs->NIndex; ++idx) { | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14223:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 14223 | for (unsigned atm = 0; atm < new_obj->NAtom; ++atm) { | ~~~~^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:52: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:100:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 100 | else \ | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14324:7: note: in expansion of macro ‘ListDelete’ 14324 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:102:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 102 | (Elem)->Link = nullptr; \ | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14324:7: note: in expansion of macro ‘ListDelete’ 14324 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In lambda function: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:100:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 100 | else \ | ^~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14336:7: note: in expansion of macro ‘ListDelete’ 14336 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:102:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 102 | (Elem)->Link = nullptr; \ | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ListMacros.h:141:4: note: in expansion of macro ‘ListDetach’ 141 | ListDetach(List,copy,Link,ElemType); \ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:14336:7: note: in expansion of macro ‘ListDelete’ 14336 | ListDelete(I->Spec, rec, next, SpecRec); /* NOTE: order N in list length! TO FIX */ | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::click(int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15027:68: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15027 | if(((panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15028:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15028 | ((!panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > panel->nest_level)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::release(int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15316:65: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15316 | (((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15317:66: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15317 | ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15458:70: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15458 | if(((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15459:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15459 | ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:15494:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 15494 | if(!((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.h:27: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CExecutive’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:16446:3: note: in expansion of macro ‘DeleteP’ 16446 | DeleteP(G->Executive); | ^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSliceNew(PyMOLGlobals*, const char*, const char*, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:16757:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16757 | if(map_state >= mapObj->State.size()) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In instantiation of ‘ExecutiveUpdateObjectsImpl(PyMOLGlobals*, const pymol::CObject&, std::unordered_set&):: [with auto:11 = ObjectMolecule*; auto:12 = const ObjectDist*]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:17125:27: 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:11 = const ObjectMolecule*; auto:12 = ObjectDist*]’: required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:17134:27: 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]’: required from ‘pymol::TrackerAdapter::iterator pymol::TrackerAdapter::begin() [with T = SpecRec; iterator = pymol::TrackerAdapter::TrackerAdapterIterator]’ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/TrackerList.h:99:29: 99 | iterator begin() { return iterator(m_tracker, m_list_id); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:204:62: 204 | for (auto& rec : ExecutiveGetSpecRecsFromPattern(G, pattern)) { | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/TrackerList.h:80:15: warning: ‘pymol::TrackerAdapter::TrackerAdapterIterator::m_tracker’ will be initialized after [-Wreorder] 80 | CTracker* m_tracker; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/TrackerList.h:79:9: warning: ‘int pymol::TrackerAdapter::TrackerAdapterIterator::m_iter_id’ [-Wreorder] 79 | int m_iter_id = -1; | ^~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/TrackerList.h:35:14: warning: when initialized here [-Wreorder] 35 | explicit TrackerAdapterIterator(CTracker* tracker, int list_id) | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp: In function ‘EditorPrepareDrag(PyMOLGlobals*, pymol::CObject*, int, int, int, int)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:1935:29: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] 1935 | " Editor: grabbing (%s).", name ENDFB(G); | ^~ ~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Editor.cpp:42: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/Feedback.h:274:15: note: ‘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, 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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++) { | ~~^~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 function ‘ExecutiveGetAdjustedSelectionWidth(PyMOLGlobals*, bool)’, inlined from ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’ at /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:8414:50: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:8192:36: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 8192 | width = static_cast(width * 1.44f); | ~~~~~~^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘ExecutiveRenderSelections(PyMOLGlobals*, int, int, GridInfo*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp:8180:7: note: ‘width’ was declared here 8180 | int width; | ^~~~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/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, | ^~~~~~~~~~ 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, | ^~~~~~~~~~ /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/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, | ^ /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, | ^ 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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, from /usr/include/c++/16/bits/locale_classes.h:43, from /usr/include/c++/16/bits/ios_base.h:43, from /usr/include/c++/16/ios:46, from /usr/include/c++/16/bits/ostream.h:43, from /usr/include/c++/16/bits/unique_ptr.h:42, from /usr/include/c++/16/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/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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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/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/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/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); | ^~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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, | ^ /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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ‘int SelectorResidueVLAsTo3DMatchScores(PyMOLGlobals*, CMatch*, int*, int, int, int*, int, int, float, float, float, float, float, float)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:813:17: warning: variable ‘cnt’ set but not used [-Wunused-but-set-variable=] 813 | int cnt = 0; | ^~~ /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:9059:11: warning: variable ‘c’ set but not used [-Wunused-but-set-variable=] 9059 | int c = 0; | ^ /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/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, | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, float, float*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:10201:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10201 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, float*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:10483:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10483 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:10507:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10507 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp: In function ‘DistSet* SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, int, int, float*, int*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:10712:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10712 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Selector.cpp:10789:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10789 | for(a = cNDummyAtoms; a < I->Table.size(); a++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/Executive.cpp: In function ‘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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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, | ^ 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; | ^~ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 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]’: required from ‘PyObject* APIResult(PyMOLGlobals*, pymol::Result&) [with T = std::array; PyObject = _object]’ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp:365:27: 365 | return PConvToPyObject(res.result()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ required from here /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/Cmd.cpp:4017:19: 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) { | ~~^~~ In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/vla.h:7, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Symmetry.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/PyMOLObject.h:26, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2/ObjectMolecule.h:24, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/P.h:22, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp:31: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/MemoryDebug.h:74:32: warning: deleting object of polymorphic class type ‘CPopUp’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 74 | #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=nullptr;}} /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4/PopUp.cpp:402:3: note: in expansion of macro ‘DeleteP’ 402 | DeleteP(I); | ^~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3/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:974, from /usr/include/c++/16/cstdio:47, from /usr/include/c++/16/ext/string_conversions.h:47, from /usr/include/c++/16/bits/basic_string.h:4465, from /usr/include/c++/16/string:58, 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 ()); | ~~~~~~~~~~~~~~~~~ /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, | ^ [ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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, | ^ 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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 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-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -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.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1/Scene.h:29, from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5/main.cpp:53: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 88%] Building CXX object 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-I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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_Event.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Event.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Event.cpp [ 90%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_Executive.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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_Image.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_Image.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_Image.cpp [ 91%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_List.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/mmtf-c -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest -I/usr/lib64/python3.14/site-packages/numpy/_core/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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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-D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer2 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer3 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer4 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer5 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/generated -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src 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-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -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_ScrollBar.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_ScrollBar.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_ScrollBar.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ScrollBar.cpp [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST 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CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_ShaderPreprocessor.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ShaderPreprocessor.cpp [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/include -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/ov/src -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0 -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer1 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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/layerCTest/Test_SymOp.cpp.o -MF CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o.d -o CMakeFiles/_cmd.dir/layerCTest/Test_SymOp.cpp.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_SymOp.cpp In file included from /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layerCTest/Test_ShaderPreprocessor.cpp:5: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h: In constructor ‘CShaderPrg::CShaderPrg(PyMOLGlobals*, const std::string&, const std::string&, const std::string&, pymol::copyable_ptr, pymol::copyable_ptr)’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:65:49: warning: ‘CShaderPrg::tessParams’ will be initialized after [-Wreorder] 65 | pymol::copyable_ptr tessParams; | ^~~~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:63:27: warning: ‘const std::string CShaderPrg::vertfile’ [-Wreorder] 63 | const std::string name, vertfile, fragfile; | ^~~~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/layer0/ShaderMgr.h:73:3: warning: when initialized here [-Wreorder] 73 | CShaderPrg(PyMOLGlobals* G_, const std::string& name, | ^~~~~~~~~~ [ 93%] Building CXX object CMakeFiles/_cmd.dir/layerCTest/Test_TTT.cpp.o /usr/bin/g++ -DMMTF_MSGPACK_USE_CPP11 -DMSGPACK_NO_BOOST -DPYMOL_OPENMP -D_HAVE_LIBXML -D_PYMOL_CTEST -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -D_cmd_EXPORTS -I/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/include 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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); | ^ 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 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/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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset 4 into destination object ‘nx’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:11: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 4 into destination object ‘ny’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [8, 12] into destination object ‘ny’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset 8 into destination object ‘ny’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:15: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 4 into destination object ‘nz’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [8, 12] into destination object ‘nz’ of size 4 1494 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset 8 into destination object ‘nz’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘handle_posn_momentum_v1’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1494:19: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 4 into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 4 into destination object ‘nx’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [8, 12] into destination object ‘nx’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset 8 into destination object ‘nx’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:13: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 4 into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 4 into destination object ‘ny’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [8, 12] into destination object ‘ny’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset 8 into destination object ‘ny’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:17: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset 4 into destination object ‘nz’ of size 4 1548 | int32_t nx, ny, nz; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset 4 into destination object ‘nz’ of size 4 /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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [8, 12] into 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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [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 1 byte into a region of size 0 [-Wstringop-overflow=] 54 | dataptr[0] = dataptr[3]; | ^ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function ‘frame_from_bytes’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1548:21: note: at offset [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 /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 .dir/layer3/CifDataValueFormatter.cpp.o CMakeFiles/_cmd.dir/layer3/Editor.cpp.o CMakeFiles/_cmd.dir/layer3/Executive.cpp.o CMakeFiles/_cmd.dir/layer3/ExecutivePython.cpp.o CMakeFiles/_cmd.dir/layer3/Interactions.cpp.o CMakeFiles/_cmd.dir/layer3/MaeExportHelpers.cpp.o CMakeFiles/_cmd.dir/layer3/MoleculeExporter.cpp.o CMakeFiles/_cmd.dir/layer3/MovieScene.cpp.o CMakeFiles/_cmd.dir/layer3/PlugIOManager.cpp.o CMakeFiles/_cmd.dir/layer3/RingFinder.cpp.o CMakeFiles/_cmd.dir/layer3/Seeker.cpp.o CMakeFiles/_cmd.dir/layer3/Selector.cpp.o CMakeFiles/_cmd.dir/layer3/SelectorTmp.cpp.o CMakeFiles/_cmd.dir/layer3/SpecRec.cpp.o CMakeFiles/_cmd.dir/layer3/SpecRecSpecial.cpp.o CMakeFiles/_cmd.dir/layer4/Cmd.cpp.o CMakeFiles/_cmd.dir/layer4/Menu.cpp.o CMakeFiles/_cmd.dir/layer4/PopUp.cpp.o CMakeFiles/_cmd.dir/layer5/PyMOL.cpp.o CMakeFiles/_cmd.dir/layer5/TestPyMOL.cpp.o CMakeFiles/_cmd.dir/layer5/main.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_Algorithm.cpp.o 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CMakeFiles/_cmd.dir/layerCTest/Test_type_traits.cpp.o CMakeFiles/_cmd.dir/layerCTest/Test_zstring_view.cpp.o CMakeFiles/_cmd.dir/ov/src/OVContext.cpp.o CMakeFiles/_cmd.dir/ov/src/OVHeap.cpp.o CMakeFiles/_cmd.dir/ov/src/OVHeapArray.cpp.o CMakeFiles/_cmd.dir/ov/src/OVLexicon.cpp.o CMakeFiles/_cmd.dir/ov/src/OVOneToAny.cpp.o CMakeFiles/_cmd.dir/ov/src/OVOneToOne.cpp.o CMakeFiles/_cmd.dir/ov/src/OVRandom.cpp.o CMakeFiles/_cmd.dir/ov/src/ov_utility.cpp.o -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -fopenmp -lgcc_s_asneeded -lgcc_s_asneeded gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_cmd/CMakeFiles 0 cmake 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-mno-omit-leaf-frame-pointer -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/_champ.dir/contrib/champ/list.c.o -MF CMakeFiles/_champ.dir/contrib/champ/list.c.o.d -o CMakeFiles/_champ.dir/contrib/champ/list.c.o -c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/list.c /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c: In function ‘ChampReassignLexPri’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c:3797:7: warning: variable ‘n_atom’ set but not used [-Wunused-but-set-variable=] 3797 | int n_atom; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c: In function ‘ChampStereoToInternal’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c:3966:10: warning: variable ‘n_atom’ set but not used [-Wunused-but-set-variable=] 3966 | int n_atom; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c: In function ‘ChampStereoFromInternal’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c:4049:10: warning: variable ‘n_atom’ set but not used [-Wunused-but-set-variable=] 4049 | int n_atom; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c: In function ‘ChampOrientBonds’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c:4135:7: warning: variable ‘n_atom’ set but not used [-Wunused-but-set-variable=] 4135 | int n_atom; | ^~~~~~ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c: In function ‘ChampDetectChirality’: /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/contrib/champ/champ.c:4357:10: warning: variable ‘n_atom’ set but not used [-Wunused-but-set-variable=] 4357 | int n_atom; | ^~~~~~ [ 63%] Building C object CMakeFiles/_champ.dir/contrib/champ/os_memory.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/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/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 [ 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/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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 /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)) { | ^ [ 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/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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/python3.14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_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-314/chempy/champ/_champ.cpython-314-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 -shared -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 -Wl,--dependency-file=CMakeFiles/_champ.dir/link.d -Wl,-soname,_champ.cpython-314-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-314/chempy/champ/_champ.cpython-314-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-314/_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-314/_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-314/_champ/CMakeFiles 0 running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-314/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-x86_64-cpython-314/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol2 copying modules/pymol/xwin.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/shortcut_manager.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/shortcut_dict.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/seqalign.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/save_shortcut.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/mpeg_encode.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/morphing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/lazyio.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/cgobuilder.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/_gui.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/__main__.py -> build/lib.linux-x86_64-cpython-314/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol creating build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-cpython-314/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-cpython-314/pmg_tk creating build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/shortcut_menu_gui.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/scene_bin_gui.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-x86_64-cpython-314/pmg_qt copying modules/chempy/xyz.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-cpython-314/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy creating build/lib.linux-x86_64-cpython-314/pymol_web/examples copying modules/pymol_web/examples/justhttpd.py -> build/lib.linux-x86_64-cpython-314/pymol_web/examples copying modules/pymol_web/examples/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol_web/examples creating build/lib.linux-x86_64-cpython-314/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-x86_64-cpython-314/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-x86_64-cpython-314/web/examples creating build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol/wizard creating build/lib.linux-x86_64-cpython-314/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol/stereochemistry creating build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol/plugins creating build/lib.linux-x86_64-cpython-314/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-x86_64-cpython-314/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-x86_64-cpython-314/pymol/Qt creating build/lib.linux-x86_64-cpython-314/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/startup creating build/lib.linux-x86_64-cpython-314/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/skins creating build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal creating build/lib.linux-x86_64-cpython-314/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_tk/skins/demo creating build/lib.linux-x86_64-cpython-314/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-x86_64-cpython-314/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-x86_64-cpython-314/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-x86_64-cpython-314/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_qt/syntax creating build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms creating build/lib.linux-x86_64-cpython-314/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-cpython-314/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-cpython-314/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-cpython-314/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-cpython-314/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/tinker creating build/lib.linux-x86_64-cpython-314/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-x86_64-cpython-314/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/mmtf creating build/lib.linux-x86_64-cpython-314/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/fragments creating build/lib.linux-x86_64-cpython-314/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/fast copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-cpython-314/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-cpython-314/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-cpython-314/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/champ creating build/lib.linux-x86_64-cpython-314/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-cpython-314/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-cpython-314/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-cpython-314/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-cpython-314/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-cpython-314/chempy/bmin running egg_info creating modules/pymol.egg-info writing modules/pymol.egg-info/PKG-INFO /usr/lib/python3.14/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/shortcut_menu.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/help_shortcut.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/create_shortcut.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/change_confirm.ui -> build/lib.linux-x86_64-cpython-314/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> build/lib.linux-x86_64-cpython-314/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-314/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/python3.14/site-packages/numpy/_core/include;/usr/include;/usr/include/freetype2;/usr/include/libxml2;/usr/include/python3.14;/usr/include/python3.14; -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-314-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-314/_cmd cmake --build . --config Release -j4 /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-314/_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-314/_cmd/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_cmd' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_cmd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_cmd/CMakeFiles/_cmd.dir/DependInfo.cmake "--color=" _cmd gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_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-314/_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-314/_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-314/chempy/champ -DCMAKE_BUILD_TYPE=Release -DALL_INC_DIR=contrib/champ;/usr/include/python3.14;/usr/include/python3.14; -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-314-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-314/_champ cmake --build . --config Release -j4 /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-314/_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-314/_champ/CMakeFiles /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_champ' cd /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_champ /builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_champ/CMakeFiles/_champ.dir/DependInfo.cmake "--color=" _champ gmake[2]: Leaving directory '/builddir/build/BUILD/pymol-3.1.0-build/pymol-open-source-3.1.0/build/temp.linux-x86_64-cpython-314/_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-314/_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-314/_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-314/_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-314/_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/web creating build/bdist.linux-x86_64/wheel/web/examples copying build/lib.linux-x86_64-cpython-314/web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./web/examples copying build/lib.linux-x86_64-cpython-314/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-314/pymol_web/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol_web/examples copying build/lib.linux-x86_64-cpython-314/pymol_web/examples/justhttpd.py -> build/bdist.linux-x86_64/wheel/./pymol_web/examples creating build/bdist.linux-x86_64/wheel/pmg_qt creating build/bdist.linux-x86_64/wheel/pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/askpartial.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/change_confirm.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/colors.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/create_shortcut.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/fetch.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/help_shortcut.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/load_aln.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/load_mae.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/load_map.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/load_mtz.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/load_traj.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/movieexport.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/pluginitem.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/pluginmanager.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/png.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/props.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/render.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/save_molecule.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/save_object.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/shortcut_menu.ui -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms copying build/lib.linux-x86_64-cpython-314/pmg_qt/forms/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/forms creating build/bdist.linux-x86_64/wheel/pmg_qt/syntax copying build/lib.linux-x86_64-cpython-314/pmg_qt/syntax/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-314/pmg_qt/syntax/pml.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-314/pmg_qt/syntax/pmlparser.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-314/pmg_qt/syntax/python.py -> build/bdist.linux-x86_64/wheel/./pmg_qt/syntax copying build/lib.linux-x86_64-cpython-314/pmg_qt/TextEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/advanced_settings_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/builder.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/file_dialogs.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/keymapping.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/mimic_pmg_tk.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/mimic_tk.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/properties_dialog.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/pymol_gl_widget.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/pymol_qt_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/scene_bin_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/shortcut_menu_gui.py -> build/bdist.linux-x86_64/wheel/./pmg_qt copying build/lib.linux-x86_64-cpython-314/pmg_qt/volume.py -> build/bdist.linux-x86_64/wheel/./pmg_qt creating build/bdist.linux-x86_64/wheel/pmg_tk creating build/bdist.linux-x86_64/wheel/pmg_tk/skins creating build/bdist.linux-x86_64/wheel/pmg_tk/skins/demo copying build/lib.linux-x86_64-cpython-314/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-314/pmg_tk/skins/normal/ModalWindow.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-314/pmg_tk/skins/normal/builder.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins/normal copying build/lib.linux-x86_64-cpython-314/pmg_tk/skins/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/skins creating build/bdist.linux-x86_64/wheel/pmg_tk/startup copying build/lib.linux-x86_64-cpython-314/pmg_tk/startup/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk/startup copying build/lib.linux-x86_64-cpython-314/pmg_tk/ColorEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/Demo.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/PyMOLMapLoad.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/SetEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/Setting.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/TextEditor.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/__init__.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/volume.py -> build/bdist.linux-x86_64/wheel/./pmg_tk copying build/lib.linux-x86_64-cpython-314/pmg_tk/PMGApp.py -> build/bdist.linux-x86_64/wheel/./pmg_tk creating build/bdist.linux-x86_64/wheel/pymol2 copying build/lib.linux-x86_64-cpython-314/pymol2/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol2 copying build/lib.linux-x86_64-cpython-314/pymol2/cmd2.py -> build/bdist.linux-x86_64/wheel/./pymol2 creating build/bdist.linux-x86_64/wheel/chempy creating build/bdist.linux-x86_64/wheel/chempy/bmin copying build/lib.linux-x86_64-cpython-314/chempy/bmin/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-314/chempy/bmin/commands.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-314/chempy/bmin/realtime.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-314/chempy/bmin/state.py -> build/bdist.linux-x86_64/wheel/./chempy/bmin copying build/lib.linux-x86_64-cpython-314/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-314/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-314/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-314/chempy/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/mmtf copying build/lib.linux-x86_64-cpython-314/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-314/chempy/tinker/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-314/chempy/tinker/amber.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-314/chempy/tinker/keyword.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-314/chempy/tinker/realtime.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-314/chempy/tinker/state.py -> build/bdist.linux-x86_64/wheel/./chempy/tinker copying build/lib.linux-x86_64-cpython-314/chempy/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/arc.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/bond_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/bond_mmff.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/bonds.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/brick.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/cc1.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/charge.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/cif.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/cpv.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/dictdb.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/gamess1.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/gms.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/hetatm.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/io.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/lst.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/mae.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/map.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/mass.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/mmd.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/models.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/mol.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/mol2.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/neighbor.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/pdb.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/pkl.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/place.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/protein.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/protein_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/protein_amber99.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/protein_mmff.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/protein_residues.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/sdf.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/solvate.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/water_amber.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/water_residues.py -> build/bdist.linux-x86_64/wheel/./chempy copying build/lib.linux-x86_64-cpython-314/chempy/xyz.py -> build/bdist.linux-x86_64/wheel/./chempy creating build/bdist.linux-x86_64/wheel/chempy/champ copying build/lib.linux-x86_64-cpython-314/chempy/champ/__init__.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-314/chempy/champ/amber99.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-314/chempy/champ/assign.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-314/chempy/champ/formal_charges.py -> build/bdist.linux-x86_64/wheel/./chempy/champ copying build/lib.linux-x86_64-cpython-314/chempy/champ/_champ.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./chempy/champ creating build/bdist.linux-x86_64/wheel/pymol creating build/bdist.linux-x86_64/wheel/pymol/Qt copying build/lib.linux-x86_64-cpython-314/pymol/Qt/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/Qt copying build/lib.linux-x86_64-cpython-314/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-314/pymol/plugins/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-314/pymol/plugins/installation.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-314/pymol/plugins/legacysupport.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-314/pymol/plugins/managergui.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-314/pymol/plugins/managergui_qt.py -> build/bdist.linux-x86_64/wheel/./pymol/plugins copying build/lib.linux-x86_64-cpython-314/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-314/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-314/pymol/wizard/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/annotation.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/appearance.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/benchmark.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/box.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/charge.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/cleanup.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/command.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/demo.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/density.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/distance.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/dragging.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/filter.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/label.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/measurement.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/message.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/mutagenesis.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/nucmutagenesis.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/openvr.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/pair_fit.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/pseudoatom.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/renaming.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/sculpting.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/security.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/stereodemo.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/wizard/toggle.py -> build/bdist.linux-x86_64/wheel/./pymol/wizard copying build/lib.linux-x86_64-cpython-314/pymol/__init__.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/__main__.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/_gui.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/api.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/callback.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/cgo.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/cgobuilder.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/checking.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/cmd.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/colorprinting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/colorramping.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/commanding.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/completing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/computing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/constants.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/constants_palette.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/controlling.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/creating.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/diagnosing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/editing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/editor.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/experimenting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/exporting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/externing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/feedingback.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/fitting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/gui.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/headering.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/helping.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/importing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/internal.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/invocation.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/keyboard.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/keywords.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/lazyio.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/locking.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/menu.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/monitoring.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/morphing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/movie.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/moving.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/mpeg_encode.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/parser.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/parsing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/povray.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/preset.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/pymolhttpd.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/querying.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/rpc.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/save_shortcut.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/selecting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/selector.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/seqalign.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/setting.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/shortcut.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/shortcut_dict.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/shortcut_manager.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/util.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/vfont.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/viewing.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/wizarding.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/xray.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/xwin.py -> build/bdist.linux-x86_64/wheel/./pymol copying build/lib.linux-x86_64-cpython-314/pymol/_cmd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pymol running install_egg_info Copying modules/pymol.egg-info to build/bdist.linux-x86_64/wheel/./pymol-3.1.0-py3.14.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/.pyproject-builddir/pip-modern-metadata-78wbtn26/.tmp-gwvn5m2t/pymol-3.1.0-cp314-cp314-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-314-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-314-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-cp314-cp314-linux_x86_64.whl size=45531219 sha256=c0cf7c15cb869211756687b6bca8ca8b18e1fd98b4d74f2b2dceb9ed3bd5881b Stored in directory: /builddir/.cache/pip/wheels/28/95/88/e62d4cea840024d69761f3b272db9343209ce98f1cceedba09 Successfully built pymol + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.xDHPod + 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 ++ ls /builddir/build/BUILD/pymol-3.1.0-build/pyproject-wheeldir/pymol-3.1.0-cp314-cp314-linux_x86_64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=pymol==3.1.0 + '[' -z pymol==3.1.0 ']' + TMPDIR=/builddir/build/BUILD/pymol-3.1.0-build/.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/pyproject-wheeldir pymol==3.1.0 Using pip 26.0.1 from /usr/lib/python3.14/site-packages/pip (python 3.14) Looking in links: /builddir/build/BUILD/pymol-3.1.0-build/pyproject-wheeldir Processing /builddir/build/BUILD/pymol-3.1.0-build/pyproject-wheeldir/pymol-3.1.0-cp314-cp314-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-3.1.0-14.fc45.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.14/site-packages ']' + '[' /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages '!=' /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.14/site-packages ']' + '[' -d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages ']' + site_dirs+=("/usr/lib64/python3.14/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 %dir /usr/lib64/python3.14/site-packages/pymol-3.1.0.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/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/python3.14/site-packages/pymol-3.1.0.dist-info/RECORD --output /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-record + rm -fv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol-3.1.0.dist-info/RECORD removed '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol-3.1.0.dist-info/RECORD' + rm -fv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol-3.1.0.dist-info/REQUESTED removed '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol-3.1.0.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.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-3.1.0-14.fc45.x86_64-pyproject-files --output-modules /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.x86_64-pyproject-modules --buildroot /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT --sitelib /usr/lib/python3.14/site-packages --sitearch /usr/lib64/python3.14/site-packages --python-version 3.14 --pyproject-record /builddir/build/BUILD/pymol-3.1.0-build/pymol-3.1.0-14.fc45.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/python3.14/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/python3.14/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/modules/xmlrunner/tests/testsuite.py: updating + echo '#!/bin/sh' + echo 'export PYMOL_PATH=/usr/lib64/python3.14/site-packages/pymol' + echo 'exec /usr/bin/python3 /usr/lib64/python3.14/site-packages/pymol/__init__.py "$@"' + cp -av /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chem_comp_bond-top100.cif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/setting_help.csv' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/water.pdb' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ace.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/acetylene.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ala.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/arg.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/argn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asph.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzene.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/butane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ala.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_arg.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_argn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asph.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_cys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gln.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_glu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gly.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hid.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hie.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hip.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_his.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ile.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_leu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_met.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_phe.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_pro.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ser.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_thr.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_trp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_val.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyanide.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ethylene.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formamide.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formic.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gln.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/glu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gluh.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gly.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hid.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hie.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hip.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/his.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ile.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/indane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/leu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lysn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/met.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methane.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methanol.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/napthylene.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nhh.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nitro.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nme.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ala.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_arg.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_argn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asph.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_cys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gln.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_glu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gly.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hid.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hie.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hip.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_his.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ile.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_leu.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lys.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_met.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_phe.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_pro.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ser.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_thr.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_trp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_val.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/peptide.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phe.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phosphite.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/pro.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/realtime.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ser.pkl' 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'/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpA.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpB.pkl' 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'/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/Makefile.delsci' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/chempy.prm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make99_simple.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py' -> 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'/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1hpv.r3d' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1tii.pdb' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/cgo03.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/il2.pdb' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pdb' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pkl' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/__pycache__' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr' -> 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'/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.svg' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.svg' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt' -> 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'/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/cmyk.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/hsv.ppm' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/splash.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/icons' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/icons/icon2.svg' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices/BLOSUM62' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/anaglyph_header.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tsc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tse' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/call_compute_color_for_light.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_color_for_light.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_fog_color.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.gs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.shared' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.fs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.vs' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/README.txt' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__init__.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/apbs.ui' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/creating.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/electrostatics.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/main.py' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/double.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single-right.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single.png' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/tut' '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb' -> '/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/tut/1hpv.pdb' + _target= + _symlinks=0 + _symlinks=1 + fdupes -q -n -r -p /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chem_comp_bond-top100.cif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chem_comp_bond-top100.cif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/setting_help.csv + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/setting_help.csv + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/water.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/water.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/water.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/water.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ace.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ace.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/acetylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/acetylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/butane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/butane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyanide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyanide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ethylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ethylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formamide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formamide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formic.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formic.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/indane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/indane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methanol.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methanol.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/napthylene.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/napthylene.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nhh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nhh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nitro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nitro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nme.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nme.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ala.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ala.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_arg.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_arg.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_argn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_argn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asph.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asph.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_cys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_cys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gln.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gln.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_glu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_glu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gly.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gly.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hid.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hid.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hie.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hie.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hip.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hip.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_his.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_his.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ile.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ile.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_leu.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_leu.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lys.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lys.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_met.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_met.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/peptide.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/peptide.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phe.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phe.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phosphite.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phosphite.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/pro.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/pro.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/realtime.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/realtime.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ser.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ser.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/sulfone.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/sulfone.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/thr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/thr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/tyr.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/tyr.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utp.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utp.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utpA.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utpA.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/val.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/val.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate1.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate1.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate2.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate2.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_library.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_library.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/Makefile.delsci + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/Makefile.delsci + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/chempy.prm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/chempy.prm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make99_simple.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make99_simple.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make_simple.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make_simple.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_simple.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_simple.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_wld.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_wld.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.dat + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.dat + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.inp + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.inp + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1hpv.r3d + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1hpv.r3d + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1tii.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/1tii.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/1tii.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/1tii.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/cgo03.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/cgo03.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/il2.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/il2.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/il2.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/il2.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pkl + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pkl + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/actions.json + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/actions.json + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/actions.json + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/actions.json /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/actions.json + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/actions.json + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/bindings_vive_controller.json + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/bindings_vive_controller.json + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.svg + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.svg + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/openvr/menu_splash.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/menu_splash.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_qt/icons/refresh.svg + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_qt/icons/refresh.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/icons/refresh.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_qt/styles/pymol.sty + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_qt/styles/pymol.sty + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_qt/styles/pymol.sty + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/cmyk.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/cmyk.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/hsv.ppm + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/hsv.ppm + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/splash.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/splash.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/icons/icon2.svg + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/icons/icon2.svg + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices/BLOSUM62 + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices/BLOSUM62 + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/anaglyph_header.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/anaglyph_header.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tsc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tsc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tse + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tse + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/call_compute_color_for_light.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/call_compute_color_for_light.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_color_for_light.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_color_for_light.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_fog_color.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_fog_color.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.gs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.gs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.shared + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.shared + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/default.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/label.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.fs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.fs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.vs + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.vs + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/README.txt + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/README.txt + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__init__.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__init__.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/apbs.ui + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/apbs.ui + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/creating.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/creating.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/electrostatics.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/electrostatics.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/main.py + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/main.py + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/double.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/double.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single-right.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single-right.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single.png + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/test/single.png + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/tut/1hpv.pdb + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/data/tut/1hpv.pdb + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/demo.sdf + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/demo.sdf + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms + test -z '' + _target= + continue + read _file + test -z '' + _target=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae.gz + test 1 = 1 + ln -sf /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae.gz + read _file + test -z /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz + test -z '' + _target= + continue + read _file + 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 -j4 --strict-build-id -m -i --build-id-seed 3.1.0-14.fc45 --unique-debug-suffix -3.1.0-14.fc45.x86_64 --unique-debug-src-base pymol-3.1.0-14.fc45.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -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-3.1.0-14.fc45.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/pymol-3.1.0-14.fc45.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-14.fc45.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-14.fc45.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-3.1.0-14.fc45.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit mangling shebang in /usr/bin/pymol from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.14 using python3.14 Bytecompiling .py files below /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14 using python3.14 /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:147: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py:151: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. /usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: "\=" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\="? A raw string is also an option. /usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/webgui02.py:156: SyntaxWarning: "\=" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\="? A raw string is also an option. + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j4 /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/web/examples/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol_web/examples/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol2/__pycache__/cmd2.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol_web/examples/__pycache__/justhttpd.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol2/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/__pycache__/plot_timings.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/__pycache__/conftest.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/__pycache__/make_test_stubs.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pymol/testing/tests/undo/__pycache__/conftest.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/web/examples/__pycache__/justhttpd.cpython-314.opt-1.pyc: rewriting with normalized contents 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rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/pkl.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/mmd.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/mass.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/map.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/pdb.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/neighbor.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/mol2.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/lst.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/mae.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/io.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/models.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/hetatm.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/gms.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/cc1.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/brick.cpython-314.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/cpv.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/brick.cpython-314.pyc: replacing with normalized version /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/gamess1.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pmg_qt/__pycache__/builder.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/charge.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/bond_mmff.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/bond_amber.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/arc.cpython-314.opt-1.pyc: 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/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/tinker/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/__pycache__/cif.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/fragments/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/mmtf/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/champ/__pycache__/assign.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/fast/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/tinker/__pycache__/amber.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/champ/__pycache__/formal_charges.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/bmin/__pycache__/commands.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/bmin/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/bmin/__pycache__/util.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/mmtf/__pycache__/io.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/champ/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/bmin/__pycache__/state.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/bmin/__pycache__/realtime.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/chempy/champ/__pycache__/amber99.cpython-314.opt-1.pyc: rewriting with normalized contents Scanned 218 directories and 2483 files, processed 464 inodes, 443 modified (54 replaced + 389 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr Scanned 217 directories and 2483 files, considered 2212 files, read 178 files, linked 7 files, 0 errors sum of sizes of linked files: 9973 bytes Reading /builddir/build/BUILD/pymol-3.1.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.I4ARwK + 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 + PYTHONPATH=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages:/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.14/site-packages + _PYTHONSITE=/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib64/python3.14/site-packages:/builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT/usr/lib/python3.14/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-3.1.0-14.fc45.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.LOgPwa + 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 warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chem_comp_bond-top100.cif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ace.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/acetylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/butane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_cys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gln.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_glu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gly.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hid.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hie.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hip.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_his.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ile.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_leu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_met.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_phe.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_pro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ser.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_thr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_trp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_val.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyanide.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ethylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formamide.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formic.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gln.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/glu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gluh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gly.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hid.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hie.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hip.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/his.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ile.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/indane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/leu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lysn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/met.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methanol.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/napthylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nhh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nitro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nme.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl warning: absolute symlink: 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warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices/BLOSUM62 -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/splash.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/setting_help.csv -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/anaglyph_header.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tsc -> 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/usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/default.fs -> 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/usr/lib64/python3.14/site-packages/pymol/data/shaders/line.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/line.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/README.txt -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__init__.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/apbs.ui -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/creating.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/electrostatics.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/main.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/double.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/single-right.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/single.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/tut/1hpv.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/demo.sdf -> /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/1tii.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/il2.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf -> /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/water.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb Provides: PyMOL = 3.1.0-14.fc45 application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 3.1.0-14.fc45 pymol(x86-64) = 3.1.0-14.fc45 python-pymol = 3.1.0-14.fc45 python3-pymol = 3.1.0-14.fc45 python3.14-pymol = 3.1.0-14.fc45 python3.14dist(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: (python3.14dist(numpy) < 3~~ with python3.14dist(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) libm.so.6(GLIBC_2.43)(64bit) libnetcdf.so.22()(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) = 3.14 rtld(GNU_HASH) Processing files: pymol+tests-3.1.0-14.fc45.x86_64 warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae -> /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms warning: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae.gz -> /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz Provides: pymol+tests = 3.1.0-14.fc45 pymol+tests(x86-64) = 3.1.0-14.fc45 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) = 3.14 Processing files: pymol-debugsource-3.1.0-14.fc45.x86_64 Provides: pymol-debugsource = 3.1.0-14.fc45 pymol-debugsource(x86-64) = 3.1.0-14.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-3.1.0-14.fc45.x86_64 Provides: debuginfo(build-id) = 87b6d4a312f03646f53f7749027e80dcd74cb52f debuginfo(build-id) = c3bb7506f2b12342cd92460cee8e76f774b7cf02 pymol-debuginfo = 3.1.0-14.fc45 pymol-debuginfo(x86-64) = 3.1.0-14.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(x86-64) = 3.1.0-14.fc45 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/pymol-3.1.0-build/BUILDROOT Wrote: /builddir/build/SRPMS/pymol-3.1.0-14.fc45.src.rpm Wrote: /builddir/build/RPMS/pymol-3.1.0-14.fc45.x86_64.rpm Wrote: /builddir/build/RPMS/pymol+tests-3.1.0-14.fc45.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-3.1.0-14.fc45.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-3.1.0-14.fc45.x86_64.rpm RPM build warnings: absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chem_comp_bond-top100.cif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chem_comp_bond-top100.cif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ace.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ace.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/acetylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/acetylene.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ala.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/arg.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/argn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/asph.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/atp_ttpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzene.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/benzocycloheptane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/butane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/butane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_cys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gln.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_glu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gluh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_gly.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hid.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hie.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_hip.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_his.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_his.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ile.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_leu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_lysn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_met.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_met.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_phe.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_pro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_ser.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_thr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_trp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_tyr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ct_val.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ct_val.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ctp_gtpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyanide.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyanide.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclobutane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cycloheptane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclohexane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentadiene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopentane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cyclopropane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/cys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/cys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ethylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ethylene.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formaldehyde.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formamide.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formamide.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/formic.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/formic.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gln.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gln.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/glu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/glu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gluh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gluh.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gly.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gly.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/gtp_ctpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hid.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hid.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hie.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hie.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/hip.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/hip.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/his.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/his.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ile.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ile.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/indane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/indane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/leu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/leu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/lysn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/lysn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/met.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/met.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/methanol.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/methanol.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/napthylene.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/napthylene.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nhh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nhh.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nitro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nitro.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nme.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nme.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ala.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_arg.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_argn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_asph.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_cys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gln.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_glu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gluh.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_gly.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hid.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hie.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_hip.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_hip.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_his.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_his.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ile.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_leu.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lys.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_lysn.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_met.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_met.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_phe.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_pro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_ser.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_ser.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_thr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_thr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_trp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_trp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_tyr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/nt_val.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/nt_val.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/peptide.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/peptide.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phe.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phe.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/phosphite.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/phosphite.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/pro.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/pro.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/realtime.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/realtime.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ser.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ser.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/sulfone.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/sulfone.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/thr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/thr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trifluoromethane.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/trp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/trp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/ttp_atpB.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/tyr.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/tyr.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utp.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utp.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/utpA.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/utpA.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/fragments/val.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/fragments/val.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate1.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/generate2.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_dep.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/__pycache__/sc_bb_ind.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate1.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate1.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/generate2.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/generate2.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_dep.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_bb_ind.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/sidechains/sc_library.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/Makefile.delsci -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/Makefile.delsci absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make99_simple.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/__pycache__/make_simple.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/chempy.prm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/chempy.prm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make99_simple.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make99_simple.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/make_simple.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/make_simple.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm94_rsm.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm94_rsm.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm96_rsm.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm96_rsm.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_simple.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_simple.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm99_wld.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm99_wld.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.dat -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.dat absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/tinker/parm_simple.inp -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/tinker/parm_simple.inp absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/chempy/water.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/1hpv.r3d -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1hpv.r3d absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/1tii.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/__pycache__/cgo03.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/__pycache__/cgo03.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/cgo03.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/cgo03.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/il2.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/demo/pept.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/openvr/actions.json -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/actions.json absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/openvr/bindings_vive_controller.json -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/bindings_vive_controller.json absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/openvr/hints_vive_controller.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/openvr/hints_vive_controller.svg -> 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/usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro65.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro66.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/aro67.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc3.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/cmyk.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/cmyk.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/hsv.ppm -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/hsv.ppm absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/icons/icon2.svg -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/icons/icon2.svg absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/matrices/BLOSUM62 -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/matrices/BLOSUM62 absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/pymol/splash.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/pymol/splash.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/setting_help.csv -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/setting_help.csv absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/anaglyph_header.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/anaglyph_header.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tsc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tsc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.tse -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.tse absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bezier.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bezier.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/bg.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/bg.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/call_compute_color_for_light.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_color_for_light.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_color_for_light.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/compute_fog_color.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/compute_fog_color.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.gs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.gs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.shared -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.shared absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/connector.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/connector.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/copy.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/copy.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/cylinder.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/cylinder.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/default.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/default.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/default.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/indicator.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/indicator.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/label.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/label.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/label.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/line.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/line.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/line.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/oit.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/oit.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/ramp.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/ramp.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/screen.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/screen.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/sphere.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/sphere.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/surface.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/surface.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/trilines.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/trilines.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/volume.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/volume.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/vrcontroller.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/vrcontroller.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.fs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.fs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/shaders/webgl_header.vs -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/shaders/webgl_header.vs absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/README.txt -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/README.txt absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__init__.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__init__.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/__init__.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/creating.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/electrostatics.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/__pycache__/qtwidgets.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/apbs.ui -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/apbs.ui absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/creating.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/creating.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/electrostatics.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/apbs_gui/qtwidgets.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__init__.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/__init__.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/__pycache__/main.cpython-314.pyc absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/startup/lightingsettings_gui/main.py -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/startup/lightingsettings_gui/main.py absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/double.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/double.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/single-right.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single-right.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/test/single.png -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/test/single.png absolute symlink: /usr/lib64/python3.14/site-packages/pymol/data/tut/1hpv.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/tut/1hpv.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/examples/devel/demo.sdf -> /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/1tii.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/1tii.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/il2.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/il2.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/ligs3d.sdf -> /usr/lib64/python3.14/site-packages/pymol/testing/data/ligs3d.sdf absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/pept.pkl -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/demo/pept.pkl absolute symlink: /usr/lib64/python3.14/site-packages/pymol/pymol_path/test/dat/water.pdb -> /usr/lib64/python3.14/site-packages/pymol/pymol_path/data/chempy/water.pdb absolute symlink: /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae -> /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms absolute symlink: /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.mae.gz -> /usr/lib64/python3.14/site-packages/pymol/testing/tests/api/data/foo.cms.gz Finish: rpmbuild pymol-3.1.0-14.fc45.src.rpm Finish: build phase for pymol-3.1.0-14.fc45.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1770926021.807988/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-3.1.0-14.fc45.src.rpm) Config(child) 5 minutes 55 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-debuginfo", "epoch": null, "version": "3.1.0", "release": "14.fc45", "arch": "x86_64" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "14.fc45", "arch": "src" }, { "name": "pymol", "epoch": null, "version": "3.1.0", "release": "14.fc45", "arch": "x86_64" }, { "name": "pymol+tests", "epoch": null, "version": "3.1.0", "release": "14.fc45", "arch": "x86_64" }, { "name": "pymol-debugsource", "epoch": null, "version": "3.1.0", "release": "14.fc45", "arch": "x86_64" } ] } RPMResults finished