Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c196' (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/8115066-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.0 PID: 9792 Logging PID: 9793 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8115066, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '21076a332a88ebaac6d85721c1e881437f7e19d5', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/cython-numpy-scipy-rebuild.checker/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.22.1-2', 'project_dirname': 'cython-numpy-scipy-rebuild.checker', 'project_name': 'cython-numpy-scipy-rebuild.checker', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/cython-numpy-scipy-rebuild.checker/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'psimovec/cython-numpy-scipy-rebuild.checker--psimovec', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'psimovec', 'tags': [], 'task_id': '8115066-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/cython-numpy-scipy-rebuild.checker/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/cython-numpy-scipy-rebuild.checker/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam'... Running: git checkout 21076a332a88ebaac6d85721c1e881437f7e19d5 -- cmd: ['git', 'checkout', '21076a332a88ebaac6d85721c1e881437f7e19d5', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam rc: 0 stdout: stderr: Note: switching to '21076a332a88ebaac6d85721c1e881437f7e19d5'. 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 21076a3 automatic import of python-pysam Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam 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 pysam-0.22.1.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o pysam-0.22.1.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/cython-numpy-scipy-rebuild.checker/python-pysam/pysam-0.22.1.tar.gz/md5/1ad924c322e8acaa946c2a8ed1366a82/pysam-0.22.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4534k 100 4534k 0 0 18.8M 0 --:--:-- --:--:-- --:--:-- 18.9M INFO: Reading stdout from command: md5sum pysam-0.22.1.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1728348809.986895 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.12.1, NVR = mock-5.9-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1728348809.986895 -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-7xb4k32b/python-pysam/python-pysam.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1728348809.986895/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 bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1728348809.986895/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/29320aea00754d1ab0bbc69f7d18b93f946d037226de42629e2e37282b4fffc1/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/29320aea00754d1ab0bbc69f7d18b93f946d037226de42629e2e37282b4fffc1/merged) with podman image umount 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_64-1728348809.986895/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.94-1.fc42.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc42.x86_64 dnf5-plugins-5.2.6.2-1.fc42.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 339.7 KiB/s | 7.8 KiB | 00m00s Copr repository 100% | 22.5 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 2.8 MiB/s | 515.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.32-2.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-10.fc42 fedora 5.7 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 42-0.3 fedora 19.4 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-1.fc42 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1.1-1.fc42 fedora 361.9 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build x86_64 4.19.94-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.16.0-4.fc42 fedora 4.1 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-64.fc41 fedora 386.8 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-1.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.3.6-1.fc41 fedora 2.2 MiB alternatives x86_64 1.30-1.fc41 fedora 66.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-7.fc41 fedora 153.5 KiB authselect-libs x86_64 1.5.0-7.fc41 fedora 818.3 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.1-1.fc42 fedora 27.5 MiB build-reproducibility-srpm-macros noarch 0.3.6-1.fc41 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-2.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-10.fc42 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20240927-1.git93b7251.fc42 fedora 136.8 KiB curl x86_64 8.10.1-2.fc42 fedora 453.3 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.0-17.fc41 fedora 199.3 KiB dwz x86_64 0.15-7.fc41 fedora 290.9 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB elfutils x86_64 0.191-8.fc41 fedora 2.6 MiB elfutils-debuginfod-client x86_64 0.191-8.fc41 fedora 64.9 KiB elfutils-default-yama-scope noarch 0.191-8.fc41 fedora 1.8 KiB elfutils-libelf x86_64 0.191-8.fc41 fedora 1.2 MiB elfutils-libs x86_64 0.191-8.fc41 fedora 646.2 KiB fedora-gpg-keys noarch 42-0.2 fedora 126.4 KiB fedora-release noarch 42-0.3 fedora 0.0 B fedora-release-identity-basic noarch 42-0.3 fedora 694.0 B fedora-repos noarch 42-0.2 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.2 fedora 2.2 KiB file x86_64 5.45-7.fc41 fedora 103.5 KiB file-libs x86_64 5.45-7.fc41 fedora 9.9 MiB filesystem x86_64 3.18-29.fc42 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.1-2.fc42 fedora 13.0 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-1.fc42 fedora 6.7 MiB glibc-common x86_64 2.40.9000-1.fc42 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-1.fc42 fedora 8.1 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-3.fc41 fedora 60.8 KiB jansson x86_64 2.13.1-10.fc41 fedora 88.3 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-2.fc41 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.6-1.fc42 fedora 934.8 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.70-4.fc41 fedora 220.2 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-3.fc41 fedora 67.2 KiB libcurl x86_64 8.10.1-2.fc42 fedora 838.4 KiB libeconf x86_64 0.6.2-3.fc41 fedora 58.0 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 14.2.1-4.fc42 fedora 274.6 KiB libgomp x86_64 14.2.1-4.fc42 fedora 523.8 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.63.0-1.fc42 fedora 170.1 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.7-6.fc42 fedora 181.1 KiB libsemanage x86_64 3.7-3.fc42 fedora 298.0 KiB libsepol x86_64 3.7-3.fc42 fedora 818.0 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 14.2.1-4.fc42 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.5-0.fc41 fedora 202.7 KiB libtool-ltdl x86_64 2.4.7-12.fc41 fedora 66.2 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-7.fc41 fedora 266.8 KiB libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.6-6.fc41 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-5.fc41 fedora 644.2 KiB openssl-libs x86_64 1:3.2.2-8.fc42 fedora 7.8 MiB p11-kit x86_64 0.25.5-3.fc41 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-3.fc41 fedora 391.4 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.6.1-6.fc42 fedora 1.8 MiB pam-libs x86_64 1.6.1-6.fc42 fedora 139.0 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.15.1-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.7.2-3.fc41 fedora 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.19.94-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.19.94-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.19.94-1.fc42 fedora 722.1 KiB rpm-sequoia x86_64 1.7.0-2.fc41 fedora 2.4 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.46.0-4.fc41 fedora 1.4 MiB systemd-libs x86_64 256.5-1.fc42 fedora 2.0 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-4.fc42 fedora 88.4 KiB xz-libs x86_64 1:5.6.3-1.fc42 fedora 218.3 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-41.fc41 fedora 703.2 KiB zlib-ng-compat x86_64 2.1.7-3.fc42 fedora 138.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 153 packages Total size of inbound packages is 53 MiB. Need to download 0 B. After this operation, 180 MiB extra will be used (install 180 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] bzip2-0:1.0.8-19.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] redhat-rpm-config-0:296-1.fc42.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] rpm-build-0:4.19.94-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] unzip-0:6.0-64.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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Already downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing PGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing PGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing PGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing PGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. [ 1/155] Verify package files 100% | 742.0 B/s | 153.0 B | 00m00s [ 2/155] Prepare transaction 100% | 1.7 KiB/s | 153.0 B | 00m00s [ 3/155] Installing libgcc-0:14.2.1-4. 100% | 134.9 MiB/s | 276.3 KiB | 00m00s [ 4/155] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/155] Installing publicsuffix-list- 100% | 66.7 MiB/s | 68.3 KiB | 00m00s [ 6/155] Installing fedora-release-ide 100% | 929.7 KiB/s | 952.0 B | 00m00s [ 7/155] Installing fedora-gpg-keys-0: 100% | 21.0 MiB/s | 172.2 KiB | 00m00s [ 8/155] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 9/155] Installing fedora-repos-0:42- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/155] Installing fedora-release-com 100% | 11.6 MiB/s | 23.7 KiB | 00m00s [ 11/155] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s [ 12/155] Installing setup-0:2.15.0-5.f 100% | 47.3 MiB/s | 726.1 KiB | 00m00s [ 13/155] Installing filesystem-0:3.18- 100% | 1.6 MiB/s | 212.6 KiB | 00m00s [ 14/155] Installing basesystem-0:11-21 100% | 0.0 B/s | 124.0 B | 00m00s [ 15/155] Installing pkgconf-m4-0:2.3.0 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [ 16/155] Installing pcre2-syntax-0:10. 100% | 124.1 MiB/s | 254.1 KiB | 00m00s [ 17/155] Installing ncurses-base-0:6.5 100% | 38.2 MiB/s | 351.7 KiB | 00m00s [ 18/155] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 19/155] Installing ncurses-libs-0:6.5 100% | 137.0 MiB/s | 981.8 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [ 20/155] Installing glibc-0:2.40.9000- 100% | 134.1 MiB/s | 6.7 MiB | 00m00s [ 21/155] Installing bash-0:5.2.32-2.fc 100% | 247.6 MiB/s | 8.2 MiB | 00m00s [ 22/155] Installing glibc-common-0:2.4 100% | 116.4 MiB/s | 1.0 MiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [ 23/155] Installing glibc-gconv-extra- 100% | 128.3 MiB/s | 8.2 MiB | 00m00s [ 24/155] Installing zlib-ng-compat-0:2 100% | 67.8 MiB/s | 138.8 KiB | 00m00s [ 25/155] Installing 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libnghttp2-0:1.63. 100% | 167.2 MiB/s | 171.2 KiB | 00m00s [102/155] Installing libtool-ltdl-0:2.4 100% | 65.7 MiB/s | 67.3 KiB | 00m00s [103/155] Installing coreutils-common-0 100% | 248.7 MiB/s | 11.2 MiB | 00m00s [104/155] Installing openssl-libs-1:3.2 100% | 289.9 MiB/s | 7.8 MiB | 00m00s [105/155] Installing coreutils-0:9.5-10 100% | 143.2 MiB/s | 5.7 MiB | 00m00s [106/155] Installing ca-certificates-0: 100% | 940.6 KiB/s | 2.4 MiB | 00m03s [107/155] Installing krb5-libs-0:1.21.3 100% | 127.7 MiB/s | 2.3 MiB | 00m00s [108/155] Installing libarchive-0:3.7.6 100% | 130.7 MiB/s | 936.7 KiB | 00m00s [109/155] Installing libtirpc-0:1.3.5-0 100% | 66.6 MiB/s | 204.5 KiB | 00m00s [110/155] Installing gzip-0:1.13-2.fc41 100% | 64.2 MiB/s | 394.6 KiB | 00m00s [111/155] Installing authselect-libs-0: 100% | 62.6 MiB/s | 833.2 KiB | 00m00s [112/155] Installing cracklib-0:2.9.11- 100% | 24.4 MiB/s | 250.3 KiB | 00m00s [113/155] Installing libpwquality-0:1.4 100% | 35.0 MiB/s | 430.1 KiB | 00m00s [114/155] Installing libnsl2-0:2.0.1-2. 100% | 28.8 MiB/s | 59.1 KiB | 00m00s [115/155] Installing pam-0:1.6.1-6.fc42 100% | 69.5 MiB/s | 1.9 MiB | 00m00s [116/155] Installing libssh-0:0.11.1-1. 100% | 139.6 MiB/s | 571.7 KiB | 00m00s [117/155] Installing rpm-sequoia-0:1.7. 100% | 263.0 MiB/s | 2.4 MiB | 00m00s [118/155] Installing rpm-libs-0:4.19.94 100% | 176.7 MiB/s | 723.6 KiB | 00m00s [119/155] Installing rpm-build-libs-0:4 100% | 101.3 MiB/s | 207.5 KiB | 00m00s [120/155] Installing libevent-0:2.1.12- 100% | 175.7 MiB/s | 899.5 KiB | 00m00s [121/155] Installing openldap-0:2.6.8-5 100% | 158.2 MiB/s | 648.0 KiB | 00m00s [122/155] Installing libcurl-0:8.10.1-2 100% | 205.0 MiB/s | 839.5 KiB | 00m00s [123/155] Installing elfutils-debuginfo 100% | 32.7 MiB/s | 66.9 KiB | 00m00s [124/155] Installing elfutils-0:0.191-8 100% | 232.7 MiB/s | 2.6 MiB | 00m00s [125/155] Installing binutils-0:2.43.1- 100% | 245.9 MiB/s | 27.5 MiB | 00m00s [126/155] Installing gdb-minimal-0:15.1 100% | 270.7 MiB/s | 13.0 MiB | 00m00s [127/155] Installing debugedit-0:5.0-17 100% | 98.6 MiB/s | 202.0 KiB | 00m00s [128/155] Installing curl-0:8.10.1-2.fc 100% | 22.3 MiB/s | 455.8 KiB | 00m00s [129/155] Installing rpm-0:4.19.94-1.fc 100% | 89.5 MiB/s | 2.5 MiB | 00m00s [130/155] Installing efi-srpm-macros-0: 100% | 20.1 MiB/s | 41.2 KiB | 00m00s [131/155] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [132/155] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [133/155] Installing rust-srpm-macros-0 100% | 5.4 MiB/s | 5.6 KiB | 00m00s [134/155] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [135/155] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [136/155] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [137/155] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [138/155] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [139/155] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [140/155] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [141/155] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [142/155] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [143/155] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [144/155] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [145/155] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [146/155] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [147/155] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [148/155] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [149/155] Installing redhat-rpm-config- 100% | 62.9 MiB/s | 193.2 KiB | 00m00s [150/155] Installing rpm-build-0:4.19.9 100% | 49.5 MiB/s | 202.9 KiB | 00m00s [151/155] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [152/155] Installing util-linux-0:2.40. 100% | 88.5 MiB/s | 3.7 MiB | 00m00s [153/155] Installing authselect-0:1.5.0 100% | 38.6 MiB/s | 157.9 KiB | 00m00s [154/155] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [155/155] Installing info-0:7.1.1-1.fc4 100% | 117.2 KiB/s | 362.3 KiB | 00m03s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-1.fc41.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-7.fc41.x86_64 authselect-libs-1.5.0-7.fc41.x86_64 basesystem-11-21.fc41.noarch bash-5.2.32-2.fc42.x86_64 binutils-2.43.1-1.fc42.x86_64 build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-2.fc42.noarch coreutils-9.5-10.fc42.x86_64 coreutils-common-9.5-10.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20240927-1.git93b7251.fc42.noarch curl-8.10.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.0-17.fc41.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-7.fc41.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.191-8.fc41.x86_64 elfutils-debuginfod-client-0.191-8.fc41.x86_64 elfutils-default-yama-scope-0.191-8.fc41.noarch elfutils-libelf-0.191-8.fc41.x86_64 elfutils-libs-0.191-8.fc41.x86_64 fedora-gpg-keys-42-0.2.noarch fedora-release-42-0.3.noarch fedora-release-common-42-0.3.noarch fedora-release-identity-basic-42-0.3.noarch fedora-repos-42-0.2.noarch fedora-repos-rawhide-42-0.2.noarch file-5.45-7.fc41.x86_64 file-libs-5.45-7.fc41.x86_64 filesystem-3.18-29.fc42.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.1-2.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-1.fc42.x86_64 glibc-common-2.40.9000-1.fc42.x86_64 glibc-gconv-extra-2.40.9000-1.fc42.x86_64 glibc-minimal-langpack-2.40.9000-1.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-3.fc41.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1.1-1.fc42.x86_64 jansson-2.13.1-10.fc41.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-2.fc41.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.6-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.70-4.fc41.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-3.fc41.x86_64 libcurl-8.10.1-2.fc42.x86_64 libeconf-0.6.2-3.fc41.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-14.2.1-4.fc42.x86_64 libgomp-14.2.1-4.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.63.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.7-6.fc42.x86_64 libsemanage-3.7-3.fc42.x86_64 libsepol-3.7-3.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-4.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.5-0.fc41.x86_64 libtool-ltdl-2.4.7-12.fc41.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-7.fc41.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.6-6.fc41.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-5.fc41.x86_64 openssl-libs-3.2.2-8.fc42.x86_64 p11-kit-0.25.5-3.fc41.x86_64 p11-kit-trust-0.25.5-3.fc41.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-6.fc42.x86_64 pam-libs-1.6.1-6.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.15.1-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.7.2-3.fc41.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-296-1.fc42.noarch rpm-4.19.94-1.fc42.x86_64 rpm-build-4.19.94-1.fc42.x86_64 rpm-build-libs-4.19.94-1.fc42.x86_64 rpm-libs-4.19.94-1.fc42.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.16.0-4.fc42.x86_64 sqlite-libs-3.46.0-4.fc41.x86_64 systemd-libs-256.5-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-64.fc41.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-4.fc42.x86_64 xz-5.6.3-1.fc42.x86_64 xz-libs-5.6.3-1.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.1.7-3.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.1-2.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1728348809.986895/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-7xb4k32b/python-pysam/python-pysam.spec) Config(child) 0 minutes 22 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/python-pysam-0.22.1-2.fc42.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1728348809.986895/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1728348809.986895/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_64-1728348809.986895/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.94-1.fc42.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc42.x86_64 dnf5-plugins-5.2.6.2-1.fc42.x86_64 Finish: chroot init Start: build phase for python-pysam-0.22.1-2.fc42.src.rpm Start: build setup for python-pysam-0.22.1-2.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.1-2.fc42.src.rpm Updating and loading repositories: Copr repository 100% | 27.8 KiB/s | 1.5 KiB | 00m00s fedora 100% | 390.6 KiB/s | 7.8 KiB | 00m00s Copr repository 100% | 3.0 MiB/s | 515.9 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel x86_64 1.0.8-19.fc41 fedora 309.8 KiB gcc x86_64 14.2.1-4.fc42 fedora 104.4 MiB python3-cython x86_64 3.0.11-1.fc41 fedora 18.1 MiB python3-devel x86_64 3.13.0~rc3-1.fc42 fedora 1.8 MiB python3-setuptools noarch 69.2.0-8.fc41 fedora 7.2 MiB python3-sphinx noarch 1:7.3.7-2.fc41 fedora 10.8 MiB python3-sphinx_rtd_theme noarch 2.0.0-9.fc42 fedora 317.9 KiB xz-devel x86_64 1:5.6.3-1.fc42 fedora 255.6 KiB zlib-ng-compat-devel x86_64 2.1.7-3.fc42 fedora 106.8 KiB Installing dependencies: annobin-docs noarch 12.70-1.fc42 fedora 97.7 KiB annobin-plugin-gcc x86_64 12.70-1.fc42 fedora 985.6 KiB cmake-filesystem x86_64 3.28.3-7.fc41 fedora 0.0 B cpp x86_64 14.2.1-4.fc42 fedora 35.0 MiB expat x86_64 2.6.3-1.fc42 fedora 291.5 KiB fontawesome4-fonts noarch 1:4.7.0-23.fc41 fedora 296.6 KiB fonts-filesystem noarch 1:2.0.5-17.fc41 fedora 0.0 B gcc-plugin-annobin x86_64 14.2.1-4.fc42 fedora 61.1 KiB glibc-devel x86_64 2.40.9000-1.fc42 fedora 37.8 KiB glibc-headers-x86 noarch 2.40.9000-1.fc42 fedora 2.2 MiB google-roboto-slab-fonts noarch 1.100263-0.24.20150923git.fc41 fedora 699.6 KiB kernel-headers x86_64 6.11.0-63.fc42 fedora 6.4 MiB lato-fonts noarch 2.015-22.fc41 fedora 11.3 MiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libxcrypt-devel x86_64 4.4.36-7.fc41 fedora 30.3 KiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB pyproject-rpm-macros noarch 1.15.1-1.fc42 fedora 109.2 KiB python-pip-wheel noarch 24.2-2.fc42 fedora 1.2 MiB python-rpm-macros noarch 3.13-3.fc41 fedora 22.1 KiB python3 x86_64 3.13.0~rc3-1.fc42 fedora 31.8 KiB python3-babel noarch 2.16.0-1.fc42 fedora 28.3 MiB python3-charset-normalizer noarch 3.3.2-5.fc41 fedora 314.8 KiB python3-docutils noarch 0.21.2-1.fc42 fedora 4.9 MiB python3-idna noarch 3.9-1.fc42 fedora 639.8 KiB python3-imagesize noarch 1.4.1-9.fc41 fedora 35.3 KiB python3-jinja2 noarch 3.1.4-5.fc41 fedora 2.9 MiB python3-libs x86_64 3.13.0~rc3-1.fc42 fedora 40.4 MiB python3-markupsafe x86_64 2.1.5-3.fc41 fedora 57.5 KiB python3-packaging noarch 24.1-2.fc41 fedora 422.3 KiB python3-pygments noarch 2.18.0-2.fc42 fedora 10.6 MiB python3-requests noarch 2.32.3-3.fc41 fedora 485.9 KiB python3-rpm-generators noarch 14-11.fc41 fedora 81.7 KiB python3-rpm-macros noarch 3.13-3.fc41 fedora 6.4 KiB python3-snowballstemmer noarch 2.2.0-13.fc41 fedora 1.7 MiB python3-sphinx-theme-alabaster noarch 0.7.16-6.fc41 fedora 41.9 KiB python3-sphinxcontrib-jquery noarch 4.1-9.fc41 fedora 381.8 KiB python3-urllib3 noarch 2.2.3-3.fc42 fedora 1.0 MiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB Transaction Summary: Installing: 49 packages Total size of inbound packages is 89 MiB. Need to download 89 MiB. After this operation, 298 MiB extra will be used (install 298 MiB, remove 0 B). [ 1/49] python3-sphinx_rtd_theme-0:2.0. 100% | 456.6 KiB/s | 84.0 KiB | 00m00s [ 2/49] python3-setuptools-0:69.2.0-8.f 100% | 6.7 MiB/s | 1.6 MiB | 00m00s [ 3/49] python3-cython-0:3.0.11-1.fc41. 100% | 9.0 MiB/s | 3.9 MiB | 00m00s [ 4/49] bzip2-devel-0:1.0.8-19.fc41.x86 100% | 3.5 MiB/s | 213.7 KiB | 00m00s [ 5/49] python3-sphinx-1:7.3.7-2.fc41.n 100% | 16.1 MiB/s | 2.6 MiB | 00m00s [ 6/49] python3-devel-0:3.13.0~rc3-1.fc 100% | 4.1 MiB/s | 402.4 KiB | 00m00s [ 7/49] xz-devel-1:5.6.3-1.fc42.x86_64 100% | 1.2 MiB/s | 66.4 KiB | 00m00s [ 8/49] zlib-ng-compat-devel-0:2.1.7-3. 100% | 692.6 KiB/s | 38.1 KiB | 00m00s [ 9/49] libmpc-0:1.3.1-6.fc41.x86_64 100% | 1.2 MiB/s | 71.1 KiB | 00m00s [10/49] make-1:4.4.1-9.fc42.x86_64 100% | 5.7 MiB/s | 586.3 KiB | 00m00s [11/49] fontawesome4-fonts-1:4.7.0-23.f 100% | 3.7 MiB/s | 204.5 KiB | 00m00s [12/49] google-roboto-slab-fonts-0:1.10 100% | 4.2 MiB/s | 239.0 KiB | 00m00s [13/49] lato-fonts-0:2.015-22.fc41.noar 100% | 10.1 MiB/s | 3.1 MiB | 00m00s [14/49] cpp-0:14.2.1-4.fc42.x86_64 100% | 18.2 MiB/s | 11.9 MiB | 00m01s [15/49] gcc-0:14.2.1-4.fc42.x86_64 100% | 27.1 MiB/s | 37.0 MiB | 00m01s [16/49] python3-docutils-0:0.21.2-1.fc4 100% | 6.7 MiB/s | 1.1 MiB | 00m00s [17/49] python3-sphinxcontrib-jquery-0: 100% | 1.1 MiB/s | 114.0 KiB | 00m00s [18/49] python3-imagesize-0:1.4.1-9.fc4 100% | 363.2 KiB/s | 22.2 KiB | 00m00s [19/49] python3-jinja2-0:3.1.4-5.fc41.n 100% | 5.5 MiB/s | 492.8 KiB | 00m00s [20/49] python3-packaging-0:24.1-2.fc41 100% | 2.3 MiB/s | 125.4 KiB | 00m00s [21/49] python3-requests-0:2.32.3-3.fc4 100% | 2.6 MiB/s | 159.4 KiB | 00m00s [22/49] python3-babel-0:2.16.0-1.fc42.n 100% | 23.9 MiB/s | 6.5 MiB | 00m00s [23/49] python3-snowballstemmer-0:2.2.0 100% | 3.9 MiB/s | 258.4 KiB | 00m00s [24/49] python3-pygments-0:2.18.0-2.fc4 100% | 15.2 MiB/s | 2.5 MiB | 00m00s [25/49] python3-sphinx-theme-alabaster- 100% | 457.6 KiB/s | 24.3 KiB | 00m00s [26/49] cmake-filesystem-0:3.28.3-7.fc4 100% | 364.9 KiB/s | 18.2 KiB | 00m00s [27/49] fonts-filesystem-1:2.0.5-17.fc4 100% | 169.7 KiB/s | 8.5 KiB | 00m00s [28/49] python3-markupsafe-0:2.1.5-3.fc 100% | 580.8 KiB/s | 30.8 KiB | 00m00s [29/49] python3-charset-normalizer-0:3. 100% | 1.7 MiB/s | 107.1 KiB | 00m00s [30/49] python3-idna-0:3.9-1.fc42.noarc 100% | 1.5 MiB/s | 117.9 KiB | 00m00s [31/49] python3-urllib3-0:2.2.3-3.fc42. 100% | 3.3 MiB/s | 277.8 KiB | 00m00s [32/49] expat-0:2.6.3-1.fc42.x86_64 100% | 1.8 MiB/s | 114.1 KiB | 00m00s [33/49] libb2-0:0.98.1-12.fc41.x86_64 100% | 466.8 KiB/s | 25.7 KiB | 00m00s [34/49] mpdecimal-0:2.5.1-16.fc41.x86_6 100% | 1.7 MiB/s | 89.0 KiB | 00m00s [35/49] python-pip-wheel-0:24.2-2.fc42. 100% | 11.8 MiB/s | 1.2 MiB | 00m00s [36/49] tzdata-0:2024a-9.fc41.noarch 100% | 5.3 MiB/s | 714.7 KiB | 00m00s [37/49] python3-0:3.13.0~rc3-1.fc42.x86 100% | 365.3 KiB/s | 27.8 KiB | 00m00s [38/49] glibc-devel-0:2.40.9000-1.fc42. 100% | 2.0 MiB/s | 135.6 KiB | 00m00s [39/49] glibc-headers-x86-0:2.40.9000-1 100% | 9.6 MiB/s | 627.7 KiB | 00m00s [40/49] libxcrypt-devel-0:4.4.36-7.fc41 100% | 506.3 KiB/s | 28.9 KiB | 00m00s [41/49] python3-libs-0:3.13.0~rc3-1.fc4 100% | 15.6 MiB/s | 9.1 MiB | 00m01s [42/49] gcc-plugin-annobin-0:14.2.1-4.f 100% | 904.6 KiB/s | 55.2 KiB | 00m00s [43/49] annobin-plugin-gcc-0:12.70-1.fc 100% | 9.1 MiB/s | 971.7 KiB | 00m00s [44/49] kernel-headers-0:6.11.0-63.fc42 100% | 12.1 MiB/s | 1.6 MiB | 00m00s [45/49] annobin-docs-0:12.70-1.fc42.noa 100% | 1.3 MiB/s | 92.0 KiB | 00m00s [46/49] pyproject-rpm-macros-0:1.15.1-1 100% | 772.8 KiB/s | 43.3 KiB | 00m00s [47/49] python-rpm-macros-0:3.13-3.fc41 100% | 289.6 KiB/s | 17.7 KiB | 00m00s [48/49] python3-rpm-generators-0:14-11. 100% | 412.7 KiB/s | 29.3 KiB | 00m00s [49/49] python3-rpm-macros-0:3.13-3.fc4 100% | 159.5 KiB/s | 12.4 KiB | 00m00s -------------------------------------------------------------------------------- [49/49] Total 100% | 35.8 MiB/s | 88.7 MiB | 00m02s Running transaction [ 1/51] Verify package files 100% | 167.0 B/s | 49.0 B | 00m00s [ 2/51] Prepare transaction 100% | 445.0 B/s | 49.0 B | 00m00s [ 3/51] Installing python-rpm-macros-0: 100% | 22.3 MiB/s | 22.8 KiB | 00m00s [ 4/51] Installing fonts-filesystem-1:2 100% | 0.0 B/s | 788.0 B | 00m00s [ 5/51] Installing python3-rpm-macros-0 100% | 0.0 B/s | 6.7 KiB | 00m00s [ 6/51] Installing libmpc-0:1.3.1-6.fc4 100% | 81.1 MiB/s | 166.2 KiB | 00m00s [ 7/51] Installing cpp-0:14.2.1-4.fc42. 100% | 291.7 MiB/s | 35.0 MiB | 00m00s [ 8/51] Installing pyproject-rpm-macros 100% | 108.6 MiB/s | 111.2 KiB | 00m00s [ 9/51] Installing fontawesome4-fonts-1 100% | 145.4 MiB/s | 297.8 KiB | 00m00s [10/51] Installing google-roboto-slab-f 100% | 114.2 MiB/s | 701.4 KiB | 00m00s [11/51] Installing lato-fonts-0:2.015-2 100% | 306.3 MiB/s | 11.3 MiB | 00m00s [12/51] Installing annobin-docs-0:12.70 100% | 32.2 MiB/s | 98.8 KiB | 00m00s [13/51] Installing kernel-headers-0:6.1 100% | 105.5 MiB/s | 6.5 MiB | 00m00s [14/51] Installing glibc-headers-x86-0: 100% | 91.4 MiB/s | 2.3 MiB | 00m00s [15/51] Installing libxcrypt-devel-0:4. 100% | 15.9 MiB/s | 32.6 KiB | 00m00s [16/51] Installing glibc-devel-0:2.40.9 100% | 6.8 MiB/s | 41.5 KiB | 00m00s [17/51] Installing tzdata-0:2024a-9.fc4 100% | 27.3 MiB/s | 1.9 MiB | 00m00s [18/51] Installing python-pip-wheel-0:2 100% | 413.9 MiB/s | 1.2 MiB | 00m00s [19/51] Installing mpdecimal-0:2.5.1-16 100% | 201.2 MiB/s | 206.0 KiB | 00m00s [20/51] Installing libb2-0:0.98.1-12.fc 100% | 42.3 MiB/s | 43.3 KiB | 00m00s [21/51] Installing expat-0:2.6.3-1.fc42 100% | 35.8 MiB/s | 293.6 KiB | 00m00s [22/51] Installing python3-libs-0:3.13. 100% | 194.9 MiB/s | 40.7 MiB | 00m00s [23/51] Installing python3-0:3.13.0~rc3 100% | 16.4 MiB/s | 33.6 KiB | 00m00s [24/51] Installing python3-docutils-0:0 100% | 136.4 MiB/s | 5.0 MiB | 00m00s [25/51] Installing python3-packaging-0: 100% | 84.6 MiB/s | 433.2 KiB | 00m00s [26/51] Installing python3-idna-0:3.9-1 100% | 157.7 MiB/s | 646.1 KiB | 00m00s [27/51] Installing python3-urllib3-0:2. 100% | 111.3 MiB/s | 1.0 MiB | 00m00s [28/51] Installing python3-rpm-generato 100% | 27.0 MiB/s | 82.9 KiB | 00m00s [29/51] Installing python3-babel-0:2.16 100% | 203.6 MiB/s | 28.5 MiB | 00m00s [30/51] Installing python3-imagesize-0: 100% | 9.4 MiB/s | 38.3 KiB | 00m00s [31/51] Installing python3-pygments-0:2 100% | 161.8 MiB/s | 10.8 MiB | 00m00s [32/51] Installing python3-snowballstem 100% | 193.8 MiB/s | 1.7 MiB | 00m00s [33/51] Installing python3-sphinx-theme 100% | 22.7 MiB/s | 46.4 KiB | 00m00s [34/51] Installing python3-markupsafe-0 100% | 8.6 MiB/s | 61.5 KiB | 00m00s [35/51] Installing python3-jinja2-0:3.1 100% | 193.7 MiB/s | 2.9 MiB | 00m00s [36/51] Installing python3-charset-norm 100% | 63.4 MiB/s | 324.7 KiB | 00m00s [37/51] Installing python3-requests-0:2 100% | 69.5 MiB/s | 498.0 KiB | 00m00s [38/51] Installing python3-sphinx-1:7.3 100% | 124.0 MiB/s | 11.0 MiB | 00m00s [39/51] Installing python3-sphinxcontri 100% | 94.0 MiB/s | 385.0 KiB | 00m00s [40/51] Installing cmake-filesystem-0:3 100% | 2.3 MiB/s | 7.1 KiB | 00m00s [41/51] Installing make-1:4.4.1-9.fc42. 100% | 163.7 MiB/s | 1.8 MiB | 00m00s [42/51] Installing gcc-0:14.2.1-4.fc42. 100% | 281.4 MiB/s | 104.4 MiB | 00m00s [43/51] Installing annobin-plugin-gcc-0 100% | 34.4 MiB/s | 987.3 KiB | 00m00s [44/51] Installing gcc-plugin-annobin-0 100% | 2.3 MiB/s | 62.6 KiB | 00m00s [45/51] Installing zlib-ng-compat-devel 100% | 52.9 MiB/s | 108.3 KiB | 00m00s [46/51] Installing python3-sphinx_rtd_t 100% | 27.5 MiB/s | 338.4 KiB | 00m00s [47/51] Installing python3-devel-0:3.13 100% | 95.5 MiB/s | 1.8 MiB | 00m00s [48/51] Installing python3-cython-0:3.0 100% | 194.5 MiB/s | 18.3 MiB | 00m00s [49/51] Installing python3-setuptools-0 100% | 135.7 MiB/s | 7.3 MiB | 00m00s [50/51] Installing xz-devel-1:5.6.3-1.f 100% | 126.7 MiB/s | 259.4 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [51/51] Installing bzip2-devel-0:1.0.8- 100% | 1.5 MiB/s | 310.7 KiB | 00m00s Complete! Finish: build setup for python-pysam-0.22.1-2.fc42.src.rpm Start: rpmbuild python-pysam-0.22.1-2.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.uj9RqR + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + test -d /builddir/build/BUILD/python-pysam-0.22.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-pysam-0.22.1-build + /usr/bin/rm -rf /builddir/build/BUILD/python-pysam-0.22.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jgyl0B + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + cd /builddir/build/BUILD/python-pysam-0.22.1-build + rm -rf pysam-0.22.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.22.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.22.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-pysam-configure-c99.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcalignedsegment.c pysam/libcalignmentfile.c pysam/libcbcf.c pysam/libcbcftools.c pysam/libcbgzf.c pysam/libcfaidx.c pysam/libchtslib.c pysam/libcsamfile.c pysam/libcsamtools.c pysam/libctabix.c pysam/libctabixproxies.c pysam/libcutils.c pysam/libcvcf.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.501zYh + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-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-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 pysam-0.22.1 + FORCE_CYTHON=1 + 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 ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) 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 -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for library containing regcomp... configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-x86_64-cpython-313 creating build/lib.linux-x86_64-cpython-313/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/utils.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/version.py -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/config.py -> build/lib.linux-x86_64-cpython-313/pysam creating build/lib.linux-x86_64-cpython-313/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-cpython-313/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.cram' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.cram' to be distributed and are already explicitly excluding 'pysam.include.htslib.cram' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.m4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.m4' to be distributed and are already explicitly excluding 'pysam.include.htslib.m4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.os' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.os' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.os' to be distributed and are already explicitly excluding 'pysam.include.htslib.os' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/py.typed -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/version.h -> build/lib.linux-x86_64-cpython-313/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-313/pysam creating build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/README -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools creating build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-x86_64-cpython-313/pysam/include/samtools creating build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/README -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-cpython-313/pysam/include/bcftools creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/README -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/configure -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/header.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/region.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4 creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib creating build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -msse4.1 -mpopcnt -mssse3 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o ranlib libhts.a Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-cpython-313 creating build/temp.linux-x86_64-cpython-313/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-313/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-313/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libchtslib.c:2954:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 2954 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/htslib_util.o build/temp.linux-x86_64-cpython-313/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/sam_mods.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-x86_64-cpython-313/pysam/libchtslib.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-313/samtools creating build/temp.linux-x86_64-cpython-313/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-cpython-313/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra.0’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/cram_size.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-cpython-313/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/reset.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-cpython-313/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-313/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-313/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-313/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-313/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcsamtools.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ^ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^ Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-cpython-313/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/gff.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib/htslib/hts.h:37, from /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ bcftools/vcfmerge.c.pysam.c:866:27: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 866 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-cpython-313/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-cpython-313/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/gff.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-313/bcftools/version.c.pysam.o build/temp.linux-x86_64-cpython-313/pysam/libcbcftools.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcbcftools.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ bcftools/vcfmerge.c.pysam.c:866:27: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 866 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcutils.c -o build/temp.linux-x86_64-cpython-313/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c:2475:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 2475 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/pysam_util.c -o build/temp.linux-x86_64-cpython-313/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcutils.o build/temp.linux-x86_64-cpython-313/pysam/pysam_util.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcsamtools.cpython-313-x86_64-linux-gnu -lcbcftools.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcutils.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2567:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2616:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-cpython-313/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c:3788:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3788 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20536:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20536 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37172:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37172 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcalignmentfile.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcalignmentfile.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-313/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcsamfile.c:3299:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3299 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcsamfile.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcsamfile.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-cpython-313/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c:4307:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 4307 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcalignedsegment.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcalignedsegment.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-313/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c:3569:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3569 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libctabix.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libctabix.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-cpython-313/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcfaidx.c:3033:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3033 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcfaidx.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcfaidx.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcbcf.c -o build/temp.linux-x86_64-cpython-313/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c:4116:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 4116 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:85929:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85929 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:80605:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80605 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44314:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44314 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44340:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44340 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:80300:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80300 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcbcf.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcbcf.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-cpython-313/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbgzf.c:2485:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 2485 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcbgzf.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcbgzf.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-313/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabixproxies.c:3089:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3089 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libctabixproxies.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libctabixproxies.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools -I/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -I/usr/include/python3.13 -c pysam/libcvcf.c -o build/temp.linux-x86_64-cpython-313/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c:3698:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 3698 | Py_UNICODE *as_pyunicodes; | ^~~~~~~~~~ pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:30040:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 30040 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24992:10: note: ‘__pyx_v_qual’ was declared here 24992 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -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-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-313/pysam/libcvcf.o -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/pysam -L/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -Lbuild/lib.linux-x86_64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-x86_64-linux-gnu -lcutils.cpython-313-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pysam/libcvcf.cpython-313-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/build/lib.linux-x86_64-cpython-313 + PYTHONPATH=/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/build/lib.linux-x86_64-cpython-313 + sphinx-build-3 doc html Running Sphinx v7.3.7 making output directory... done [autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst loading intersphinx inventory from https://docs.python.org/3.13/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.13/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.13/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] api reading sources... [ 22%] benchmarking reading sources... [ 33%] developer reading sources... [ 44%] faq reading sources... [ 56%] glossary reading sources... [ 67%] index reading sources... [ 78%] installation reading sources... [ 89%] release reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 11%] api writing output... [ 22%] benchmarking writing output... [ 33%] developer writing output... [ 44%] faq writing output... [ 56%] glossary writing output... [ 67%] index writing output... [ 78%] installation writing output... [ 89%] release writing output... [100%] usage generating indices... genindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in html. + rm -rf html/.doctrees html/.buildinfo + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.uOxzeW + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + '[' /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build + mkdir /builddir/build/BUILD/python-pysam-0.22.1-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-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 pysam-0.22.1 + 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 ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT --prefix /usr # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) 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 -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.13/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/Pileup.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/__init__.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/bcftools.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/samtools.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/utils.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/version.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/config.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include copying build/lib.linux-x86_64-cpython-313/pysam/include/__init__.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/LICENSE -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/README -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_color.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_import.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_index.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_md.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_split.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bamtk.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bedcov.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bedidx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/bedidx.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/coverage.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/cram_size.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/cut_target.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/dict.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/faidx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/padding.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/phase.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/reference.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/reset.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_view.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sample.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/sample.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/samtools.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/splaysort.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/stats.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/version.sh -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-313/pysam/include/samtools/config.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/HMM.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/HMM.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/LICENSE -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/README -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/abuf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/abuf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bin.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/bin.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/call.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/ccall.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/cols.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/cols.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/consensus.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/convert.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/convert.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/csq.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/dist.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/dist.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/em.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/extsort.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/extsort.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/filter.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/filter.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gff.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gff.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/hclust.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/hclust.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/hex.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/kheap.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/kmin.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/kmin.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/main.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/mcall.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/mw.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/prob1.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/prob1.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/regidx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/regidx.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/reheader.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/tabix.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/utlist.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/version.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/version.sh -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-313/pysam/include/bcftools/config.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/LICENSE -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/Makefile -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/README -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/bgzf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/bgzip.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/config.h.in -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/config.mk.in -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/configure -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/configure.ac -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/errmod.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/faidx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/header.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/header.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hts.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hts_os.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htsfile.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib.mk -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/kfunc.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/kstring.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/md5.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/multipart.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/plugin.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/probaln.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/realn.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/regidx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/region.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/sam.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/tabix.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/tbx.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/textutils.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/vcf.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/version.sh -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/os.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/cram creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/os/rand.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/config.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-313/pysam/cbcftools_util.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/csamtools_util.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/htslib_util.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/htslib_util.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignedsegment.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignedsegment.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignedsegment.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignmentfile.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignmentfile.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignmentfile.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcf.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcf.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcf.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcftools.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcftools.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcftools.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbgzf.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbgzf.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcfaidx.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcfaidx.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcfaidx.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libchtslib.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libchtslib.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libchtslib.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamfile.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamfile.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamfile.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamtools.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamtools.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamtools.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabix.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabix.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabix.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabixproxies.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabixproxies.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabixproxies.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcutils.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcutils.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcutils.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcvcf.pxd -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcvcf.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcvcf.pyx -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/py.typed -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/pysam_stream.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/pysam_util.c -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/pysam_util.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/version.h -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/version.pyi -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libchtslib.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamtools.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcftools.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcutils.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignmentfile.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcsamfile.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcalignedsegment.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabix.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcfaidx.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbcf.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcbgzf.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libctabixproxies.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-x86_64-cpython-313/pysam/libcvcf.cpython-313-x86_64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/__init__.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/utils.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/Pileup.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/samtools.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/config.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-313/pysam/__pycache__/version.cpython-313.pyc -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/bcftools.py to bcftools.cpython-313.pyc byte-compiling /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/__init__.py to __init__.cpython-313.pyc writing byte-compilation script '/tmp/tmp3vzy04_u.py' /usr/bin/python3 /tmp/tmp3vzy04_u.py removing /tmp/tmp3vzy04_u.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam-0.22.1-py3.13.egg-info running install_scripts + rm -rfv /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/bin/__pycache__ + rm /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcbcf.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libchtslib.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libctabix.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcutils.pyx /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/htslib_util.c /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.22.1-2.fc42 --unique-debug-suffix -0.22.1-2.fc42.x86_64 --unique-debug-src-base python-pysam-0.22.1-2.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-pysam-0.22.1-2.fc42.x86_64 53757 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/python3.13/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.13/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.13/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.13/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/Pileup.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/config.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/bcftools.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/Pileup.cpython-313.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/samtools.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/utils.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/version.cpython-313.pyc: rewriting with normalized contents Scanned 40 directories and 787 files, processed 9 inodes, 9 modified (2 replaced + 7 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/python-pysam-0.22.1-build/SPECPARTS/rpm-debuginfo.specpart Processing files: python3-pysam-0.22.1-2.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.dIo8i7 + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + cd pysam-0.22.1 + DOCDIR=/builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python3-pysam + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/README.rst /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.ZYfNeo + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + cd pysam-0.22.1 + LICENSEDIR=/builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/COPYING /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/bcftools/LICENSE /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/htslib/LICENSE /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/samtools/LICENSE /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE Provides: bundled(bcftools) = 1.18 bundled(htslib) = 1.18 bundled(samtools) = 1.18 libcalignedsegment.cpython-313-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-313-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-313-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-313-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-313-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-313-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-313-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-313-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-313-x86_64-linux-gnu.so()(64bit) libctabix.cpython-313-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-313-x86_64-linux-gnu.so()(64bit) libcutils.cpython-313-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-313-x86_64-linux-gnu.so()(64bit) python-pysam = 0.22.1-2.fc42 python3-pysam = 0.22.1-2.fc42 python3-pysam(x86-64) = 0.22.1-2.fc42 python3.13-pysam = 0.22.1-2.fc42 python3.13dist(pysam) = 0.22.1 python3dist(pysam) = 0.22.1 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: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(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_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(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) libcbcftools.cpython-313-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-313-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-313-x86_64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) python(abi) = 3.13 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.1-2.fc42 Processing files: python3-pysam-devel-0.22.1-2.fc42.x86_64 Provides: python-pysam-devel = 0.22.1-2.fc42 python3-pysam-devel = 0.22.1-2.fc42 python3-pysam-devel(x86-64) = 0.22.1-2.fc42 python3.13-pysam-devel = 0.22.1-2.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh python(abi) = 3.13 Processing files: python-pysam-doc-0.22.1-2.fc42.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.27wGKk + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + cd pysam-0.22.1 + DOCDIR=/builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python-pysam-doc + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/html /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.1-2.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.1-2.fc42.x86_64 Provides: python-pysam-debugsource = 0.22.1-2.fc42 python-pysam-debugsource(x86-64) = 0.22.1-2.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.1-2.fc42.x86_64 Provides: debuginfo(build-id) = 006787dea0750fca55eafb7553a66da9f716483f debuginfo(build-id) = 025c57781b00fef3aece134a4ba47365f744deeb debuginfo(build-id) = 4838c87abcffdc8872bc9e3abcb6a20b20d28d1a debuginfo(build-id) = 4ca6e5bca36487c81dc905573652d1d4fa84c0f9 debuginfo(build-id) = 5045be3c02e8bf1f328971a23b7f9f4c61f3eafa debuginfo(build-id) = 5108508f4f12f8edc1bcdcc6384a06b3b7f23223 debuginfo(build-id) = 8c75fce0475e93cfadf9d2e25f0a46a502585d2d debuginfo(build-id) = 905c81d967b58115ffa60a51dc147cdab40173a1 debuginfo(build-id) = a826f4b89b211061d48465d2f3e2d30435152c18 debuginfo(build-id) = a9727af92144b63391b05037de452cf85245056b debuginfo(build-id) = ce39060f0b3b2a0081a9f640bc81b1d7a2098cf3 debuginfo(build-id) = da7a74f31b0d41c6cb23c3ded939371c1d6b9ac1 debuginfo(build-id) = ffa541cdf5a1a6aa89b30ec35893976ba78a4d00 libcalignedsegment.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcalignmentfile.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcbcf.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcbcftools.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcbgzf.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcfaidx.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libchtslib.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcsamfile.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcsamtools.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libctabix.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libctabixproxies.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcutils.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) libcvcf.cpython-313-x86_64-linux-gnu.so-0.22.1-2.fc42.x86_64.debug()(64bit) python-pysam-debuginfo = 0.22.1-2.fc42 python3-pysam-debuginfo = 0.22.1-2.fc42 python3-pysam-debuginfo(x86-64) = 0.22.1-2.fc42 python3.13-pysam-debuginfo = 0.22.1-2.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(x86-64) = 0.22.1-2.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.1-2.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.1-2.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.1-2.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.1-2.fc42.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.22.1-2.fc42.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.fzmubg + umask 022 + cd /builddir/build/BUILD/python-pysam-0.22.1-build + test -d /builddir/build/BUILD/python-pysam-0.22.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-pysam-0.22.1-build + rm -rf /builddir/build/BUILD/python-pysam-0.22.1-build + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: File listed twice: /usr/share/licenses/python3-pysam/LICENSE File listed twice: /usr/share/licenses/python3-pysam/LICENSE Finish: rpmbuild python-pysam-0.22.1-2.fc42.src.rpm Finish: build phase for python-pysam-0.22.1-2.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1728348809.986895/root/var/log/dnf5.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.22.1-2.fc42.src.rpm) Config(child) 6 minutes 59 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": "python-pysam-debugsource", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "x86_64" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "x86_64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "noarch" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "src" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "x86_64" } ] } RPMResults finished