Warning: Permanently added '3.80.148.93' (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/8070822-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64 Version: 0.73 PID: 19003 Logging PID: 19004 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 8070822, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '35fe26df43d31a813f2d361367fc4b663b5c936b', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.22.1-2', 'project_dirname': 'zlib-ng-rebase-fedora', 'project_name': 'zlib-ng-rebase-fedora', 'project_owner': 'ljavorsk', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ljavorsk/zlib-ng-rebase-fedora/fedora-rawhide-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ljavorsk/zlib-ng-rebase-fedora--ljavorsk', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'ljavorsk', 'tags': [], 'task_id': '8070822-fedora-rawhide-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam'... Running: git checkout 35fe26df43d31a813f2d361367fc4b663b5c936b -- cmd: ['git', 'checkout', '35fe26df43d31a813f2d361367fc4b663b5c936b', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam rc: 0 stdout: stderr: Note: switching to '35fe26df43d31a813f2d361367fc4b663b5c936b'. 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 35fe26d automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/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/ljavorsk/zlib-ng-rebase-fedora/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 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 4534k 100 4534k 0 0 23.5M 0 --:--:-- --:--:-- --:--:-- 23.4M INFO: Reading stdout from command: md5sum pysam-0.22.1.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727343304.927975 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727343304.927975 -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-6rdqc23s/python-pysam/python-pysam.spec) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727343304.927975/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-aarch64-bootstrap-1727343304.927975/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/1811ac4ffde70d7a142f548fca08095e5cad67d5b02ca184b763d6c52a090186/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/1811ac4ffde70d7a142f548fca08095e5cad67d5b02ca184b763d6c52a090186/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-aarch64-1727343304.927975/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.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 dnf5-5.2.6.2-1.fc42.aarch64 dnf5-plugins-5.2.6.2-1.fc42.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 237.9 KiB/s | 7.1 KiB | 00m00s Copr repository 100% | 90.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 77.4 MiB/s | 2.6 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 5.2.32-2.fc42 fedora 8.3 MiB bzip2 aarch64 1.0.8-19.fc41 fedora 427.6 KiB coreutils aarch64 9.5-9.fc42 fedora 20.8 MiB cpio aarch64 2.15-2.fc41 fedora 1.2 MiB diffutils aarch64 3.10-8.fc41 fedora 2.1 MiB fedora-release-common noarch 42-0.3 fedora 19.4 KiB findutils aarch64 1:4.10.0-4.fc41 fedora 2.1 MiB gawk aarch64 5.3.0-4.fc41 fedora 4.2 MiB glibc-minimal-langpack aarch64 2.40.9000-5.fc42 copr_base 0.0 B grep aarch64 3.11-9.fc41 fedora 1.1 MiB gzip aarch64 1.13-2.fc41 fedora 488.9 KiB info aarch64 7.1.1-1.fc42 fedora 613.6 KiB patch aarch64 2.7.6-25.fc41 fedora 390.6 KiB redhat-rpm-config noarch 295-1.fc42 fedora 186.6 KiB rpm-build aarch64 4.19.94-1.fc42 fedora 1.4 MiB sed aarch64 4.9-3.fc41 fedora 1.0 MiB shadow-utils aarch64 2:4.16.0-4.fc42 fedora 7.3 MiB tar aarch64 2:1.35-4.fc41 fedora 3.1 MiB unzip aarch64 6.0-64.fc41 fedora 726.7 KiB util-linux aarch64 2.40.2-8.fc42 fedora 16.9 MiB which aarch64 2.21-42.fc41 fedora 248.2 KiB xz aarch64 1:5.6.2-2.fc41 fedora 1.5 MiB Installing dependencies: add-determinism aarch64 0.3.6-1.fc41 fedora 2.0 MiB alternatives aarch64 1.30-1.fc41 fedora 218.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs aarch64 4.0.2-1.fc41 fedora 547.4 KiB authselect aarch64 1.5.0-7.fc41 fedora 309.5 KiB authselect-libs aarch64 1.5.0-7.fc41 fedora 931.9 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils aarch64 2.43.50-1.fc42 copr_base 32.7 MiB build-reproducibility-srpm-macros noarch 0.3.6-1.fc41 fedora 735.0 B bzip2-libs aarch64 1.0.8-19.fc41 fedora 200.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-1.fc42 fedora 2.6 MiB coreutils-common aarch64 9.5-9.fc42 fedora 11.2 MiB cracklib aarch64 2.9.11-6.fc42 copr_base 422.9 KiB crypto-policies noarch 20240828-1.git5f66e81.fc42 fedora 136.9 KiB curl aarch64 8.10.1-2.fc42 copr_base 453.3 KiB cyrus-sasl-lib aarch64 2.1.28-27.fc41 fedora 3.1 MiB debugedit aarch64 5.0-17.fc41 fedora 499.2 KiB dwz aarch64 0.15-7.fc41 fedora 386.8 KiB ed aarch64 1.20.2-2.fc41 fedora 282.8 KiB efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB elfutils aarch64 0.191-8.fc41 fedora 4.9 MiB elfutils-debuginfod-client aarch64 0.191-8.fc41 fedora 396.9 KiB elfutils-default-yama-scope noarch 0.191-8.fc41 fedora 1.8 KiB elfutils-libelf aarch64 0.191-8.fc41 fedora 1.3 MiB elfutils-libs aarch64 0.191-8.fc41 fedora 938.3 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 aarch64 5.45-7.fc42 copr_base 139.5 KiB file-libs aarch64 5.45-7.fc42 copr_base 10.0 MiB filesystem aarch64 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 0.3.2-1.fc41 fedora 39.0 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal aarch64 15.1-2.fc42 copr_base 12.9 MiB gdbm aarch64 1:1.23-7.fc41 fedora 928.5 KiB gdbm-libs aarch64 1:1.23-7.fc41 fedora 426.0 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc aarch64 2.40.9000-5.fc42 copr_base 6.2 MiB glibc-common aarch64 2.40.9000-5.fc42 copr_base 1.3 MiB glibc-gconv-extra aarch64 2.40.9000-5.fc42 copr_base 18.6 MiB gmp aarch64 1:6.3.0-2.fc41 fedora 722.0 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 aarch64 2.13.1-10.fc41 fedora 220.5 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs aarch64 1.6.3-4.fc41 fedora 226.4 KiB krb5-libs aarch64 1.21.3-2.fc41 fedora 3.3 MiB libacl aarch64 2.3.2-2.fc41 fedora 196.1 KiB libarchive aarch64 3.7.6-1.fc42 copr_base 910.8 KiB libattr aarch64 2.5.2-4.fc41 fedora 196.6 KiB libblkid aarch64 2.40.2-8.fc42 fedora 418.6 KiB libbrotli aarch64 1.1.0-5.fc41 fedora 1.1 MiB libcap aarch64 2.70-4.fc41 fedora 1.4 MiB libcap-ng aarch64 0.8.5-3.fc41 fedora 417.2 KiB libcom_err aarch64 1.47.1-3.fc41 fedora 239.3 KiB libcurl aarch64 8.10.1-2.fc42 copr_base 794.4 KiB libeconf aarch64 0.6.2-3.fc41 fedora 206.1 KiB libevent aarch64 2.1.12-14.fc41 fedora 1.5 MiB libfdisk aarch64 2.40.2-8.fc42 fedora 482.9 KiB libffi aarch64 3.4.6-3.fc42 fedora 282.4 KiB libgcc aarch64 14.2.1-3.fc42 fedora 350.2 KiB libgomp aarch64 14.2.1-3.fc42 fedora 567.3 KiB libidn2 aarch64 2.3.7-2.fc41 fedora 457.2 KiB libmount aarch64 2.40.2-8.fc42 fedora 483.9 KiB libnghttp2 aarch64 1.63.0-1.fc42 copr_base 198.2 KiB libnsl2 aarch64 2.0.1-2.fc41 fedora 222.0 KiB libpkgconf aarch64 2.3.0-1.fc42 fedora 198.1 KiB libpsl aarch64 0.21.5-4.fc41 fedora 196.6 KiB libpwquality aarch64 1.4.5-11.fc41 fedora 1.1 MiB libselinux aarch64 3.7-6.fc42 fedora 265.1 KiB libsemanage aarch64 3.7-3.fc42 fedora 361.6 KiB libsepol aarch64 3.7-3.fc42 fedora 873.9 KiB libsmartcols aarch64 2.40.2-8.fc42 fedora 288.5 KiB libssh aarch64 0.11.1-1.fc42 copr_base 585.5 KiB libssh-config noarch 0.11.1-1.fc42 copr_base 277.0 B libstdc++ aarch64 14.2.1-3.fc42 fedora 2.8 MiB libtasn1 aarch64 4.19.0-9.fc41 fedora 283.8 KiB libtirpc aarch64 1.3.5-0.fc41 fedora 274.8 KiB libtool-ltdl aarch64 2.4.7-12.fc41 fedora 222.2 KiB libunistring aarch64 1.1-8.fc41 fedora 1.8 MiB libuuid aarch64 2.40.2-8.fc42 fedora 197.5 KiB libverto aarch64 0.3.2-9.fc41 fedora 197.5 KiB libxcrypt aarch64 4.4.36-7.fc41 fedora 399.0 KiB libxml2 aarch64 2.12.8-2.fc42 copr_base 1.9 MiB libzstd aarch64 1.5.6-2.fc41 fedora 796.0 KiB lua-libs aarch64 5.4.6-6.fc41 fedora 393.1 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs aarch64 1.10.0-1.fc41 fedora 261.6 KiB mpfr aarch64 4.2.1-5.fc41 fedora 818.9 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs aarch64 6.5-2.20240629.fc41 fedora 2.2 MiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap aarch64 2.6.8-5.fc41 fedora 952.3 KiB openssl-libs aarch64 1:3.2.2-9.fc42 copr_base 6.4 MiB p11-kit aarch64 0.25.5-3.fc41 fedora 2.6 MiB p11-kit-trust aarch64 0.25.5-3.fc41 fedora 655.6 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam aarch64 1.6.1-6.fc42 fedora 11.0 MiB pam-libs aarch64 1.6.1-6.fc42 fedora 607.3 KiB pcre2 aarch64 10.44-1.fc41.1 fedora 905.5 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 aarch64 2.3.0-1.fc42 fedora 240.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config aarch64 2.3.0-1.fc42 fedora 990.0 B popt aarch64 1.19-7.fc41 fedora 272.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.15.0-1.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 aarch64 8.2-11.fc42 fedora 753.3 KiB rpm aarch64 4.19.94-1.fc42 fedora 3.9 MiB rpm-build-libs aarch64 4.19.94-1.fc42 fedora 262.7 KiB rpm-libs aarch64 4.19.94-1.fc42 fedora 798.0 KiB rpm-sequoia aarch64 1.7.0-2.fc41 fedora 2.3 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 aarch64 3.46.0-4.fc41 fedora 1.6 MiB systemd-libs aarch64 256.5-1.fc42 fedora 2.5 MiB util-linux-core aarch64 2.40.2-8.fc42 fedora 6.2 MiB xxhash-libs aarch64 0.8.2-3.fc41 fedora 212.3 KiB xz-libs aarch64 1:5.6.2-2.fc41 fedora 266.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip aarch64 3.0-41.fc41 fedora 1.1 MiB zlib-ng-compat aarch64 2.2.2-1.fc42 copr_base 197.6 KiB zstd aarch64 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 52 MiB. Need to download 0 B. After this operation, 266 MiB extra will be used (install 266 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.aarch64 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.aarch64 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-0:295-1.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.aarch6 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.aarch64 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% | 676.0 B/s | 153.0 B | 00m00s [ 2/155] Prepare transaction 100% | 2.5 KiB/s | 153.0 B | 00m00s [ 3/155] Installing libgcc-0:14.2.1-3. 100% | 171.8 MiB/s | 351.9 KiB | 00m00s [ 4/155] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/155] Installing publicsuffix-list- 100% | 0.0 B/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% | 33.6 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% | 23.1 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% | 44.3 MiB/s | 726.1 KiB | 00m00s [ 13/155] Installing filesystem-0:3.18- 100% | 2.3 MiB/s | 212.6 KiB | 00m00s [ 14/155] Installing 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warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [ 19/155] Installing glibc-0:2.40.9000- 100% | 200.0 MiB/s | 6.2 MiB | 00m00s [ 20/155] Installing bash-0:5.2.32-2.fc 100% | 307.9 MiB/s | 8.3 MiB | 00m00s [ 21/155] Installing glibc-common-0:2.4 100% | 188.5 MiB/s | 1.3 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 [ 22/155] Installing glibc-gconv-extra- 100% | 339.9 MiB/s | 18.7 MiB | 00m00s [ 23/155] Installing zlib-ng-compat-0:2 100% | 193.8 MiB/s | 198.5 KiB | 00m00s [ 24/155] Installing bzip2-libs-0:1.0.8 100% | 197.1 MiB/s | 201.9 KiB | 00m00s [ 25/155] 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libpwquality-0:1.4 100% | 158.2 MiB/s | 1.1 MiB | 00m00s [114/155] Installing libnsl2-0:2.0.1-2. 100% | 109.0 MiB/s | 223.2 KiB | 00m00s [115/155] Installing pam-0:1.6.1-6.fc42 100% | 356.1 MiB/s | 11.0 MiB | 00m00s [116/155] Installing libssh-0:0.11.1-1. 100% | 191.3 MiB/s | 587.6 KiB | 00m00s [117/155] Installing rpm-sequoia-0:1.7. 100% | 328.2 MiB/s | 2.3 MiB | 00m00s [118/155] Installing rpm-libs-0:4.19.94 100% | 260.3 MiB/s | 799.5 KiB | 00m00s [119/155] Installing rpm-build-libs-0:4 100% | 257.4 MiB/s | 263.6 KiB | 00m00s [120/155] Installing libevent-0:2.1.12- 100% | 380.8 MiB/s | 1.5 MiB | 00m00s [121/155] Installing openldap-0:2.6.8-5 100% | 233.4 MiB/s | 956.1 KiB | 00m00s [122/155] Installing libcurl-0:8.10.1-2 100% | 258.9 MiB/s | 795.5 KiB | 00m00s [123/155] Installing elfutils-debuginfo 100% | 194.8 MiB/s | 398.9 KiB | 00m00s [124/155] Installing elfutils-0:0.191-8 100% | 412.9 MiB/s | 5.0 MiB | 00m00s [125/155] Installing binutils-0:2.43.50 100% | 367.9 MiB/s | 32.7 MiB | 00m00s [126/155] Installing gdb-minimal-0:15.1 100% | 339.9 MiB/s | 12.9 MiB | 00m00s [127/155] Installing debugedit-0:5.0-17 100% | 245.1 MiB/s | 502.0 KiB | 00m00s [128/155] Installing curl-0:8.10.1-2.fc 100% | 40.5 MiB/s | 455.8 KiB | 00m00s [129/155] Installing rpm-0:4.19.94-1.fc 100% | 146.0 MiB/s | 3.4 MiB | 00m00s [130/155] Installing efi-srpm-macros-0: 100% | 40.2 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% | 0.0 B/s | 1.7 KiB | 00m00s [133/155] Installing rust-srpm-macros-0 100% | 0.0 B/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% | 2.3 MiB/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% | 0.0 B/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% | 39.4 MiB/s | 40.4 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% | 349.3 MiB/s | 1.4 MiB | 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% | 368.6 MiB/s | 17.0 MiB | 00m00s [153/155] Installing authselect-0:1.5.0 100% | 102.2 MiB/s | 313.9 KiB | 00m00s [154/155] Installing which-0:2.21-42.fc 100% | 244.5 MiB/s | 250.4 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% | 288.6 KiB/s | 614.1 KiB | 00m02s Warning: skipped PGP checks for 18 packages from repository: copr_base Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-1.fc41.aarch64 alternatives-1.30-1.fc41.aarch64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.aarch64 authselect-1.5.0-7.fc41.aarch64 authselect-libs-1.5.0-7.fc41.aarch64 basesystem-11-21.fc41.noarch bash-5.2.32-2.fc42.aarch64 binutils-2.43.50-1.fc42.aarch64 build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch bzip2-1.0.8-19.fc41.aarch64 bzip2-libs-1.0.8-19.fc41.aarch64 ca-certificates-2024.2.69_v8.0.401-1.fc42.noarch coreutils-9.5-9.fc42.aarch64 coreutils-common-9.5-9.fc42.aarch64 cpio-2.15-2.fc41.aarch64 cracklib-2.9.11-6.fc42.aarch64 crypto-policies-20240828-1.git5f66e81.fc42.noarch curl-8.10.1-2.fc42.aarch64 cyrus-sasl-lib-2.1.28-27.fc41.aarch64 debugedit-5.0-17.fc41.aarch64 diffutils-3.10-8.fc41.aarch64 dwz-0.15-7.fc41.aarch64 ed-1.20.2-2.fc41.aarch64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.191-8.fc41.aarch64 elfutils-debuginfod-client-0.191-8.fc41.aarch64 elfutils-default-yama-scope-0.191-8.fc41.noarch elfutils-libelf-0.191-8.fc41.aarch64 elfutils-libs-0.191-8.fc41.aarch64 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.fc42.aarch64 file-libs-5.45-7.fc42.aarch64 filesystem-3.18-29.fc42.aarch64 findutils-4.10.0-4.fc41.aarch64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.3.2-1.fc41.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.aarch64 gdb-minimal-15.1-2.fc42.aarch64 gdbm-1.23-7.fc41.aarch64 gdbm-libs-1.23-7.fc41.aarch64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-5.fc42.aarch64 glibc-common-2.40.9000-5.fc42.aarch64 glibc-gconv-extra-2.40.9000-5.fc42.aarch64 glibc-minimal-langpack-2.40.9000-5.fc42.aarch64 gmp-6.3.0-2.fc41.aarch64 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.aarch64 gzip-1.13-2.fc41.aarch64 info-7.1.1-1.fc42.aarch64 jansson-2.13.1-10.fc41.aarch64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.aarch64 krb5-libs-1.21.3-2.fc41.aarch64 libacl-2.3.2-2.fc41.aarch64 libarchive-3.7.6-1.fc42.aarch64 libattr-2.5.2-4.fc41.aarch64 libblkid-2.40.2-8.fc42.aarch64 libbrotli-1.1.0-5.fc41.aarch64 libcap-2.70-4.fc41.aarch64 libcap-ng-0.8.5-3.fc41.aarch64 libcom_err-1.47.1-3.fc41.aarch64 libcurl-8.10.1-2.fc42.aarch64 libeconf-0.6.2-3.fc41.aarch64 libevent-2.1.12-14.fc41.aarch64 libfdisk-2.40.2-8.fc42.aarch64 libffi-3.4.6-3.fc42.aarch64 libgcc-14.2.1-3.fc42.aarch64 libgomp-14.2.1-3.fc42.aarch64 libidn2-2.3.7-2.fc41.aarch64 libmount-2.40.2-8.fc42.aarch64 libnghttp2-1.63.0-1.fc42.aarch64 libnsl2-2.0.1-2.fc41.aarch64 libpkgconf-2.3.0-1.fc42.aarch64 libpsl-0.21.5-4.fc41.aarch64 libpwquality-1.4.5-11.fc41.aarch64 libselinux-3.7-6.fc42.aarch64 libsemanage-3.7-3.fc42.aarch64 libsepol-3.7-3.fc42.aarch64 libsmartcols-2.40.2-8.fc42.aarch64 libssh-0.11.1-1.fc42.aarch64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-3.fc42.aarch64 libtasn1-4.19.0-9.fc41.aarch64 libtirpc-1.3.5-0.fc41.aarch64 libtool-ltdl-2.4.7-12.fc41.aarch64 libunistring-1.1-8.fc41.aarch64 libuuid-2.40.2-8.fc42.aarch64 libverto-0.3.2-9.fc41.aarch64 libxcrypt-4.4.36-7.fc41.aarch64 libxml2-2.12.8-2.fc42.aarch64 libzstd-1.5.6-2.fc41.aarch64 lua-libs-5.4.6-6.fc41.aarch64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.aarch64 mpfr-4.2.1-5.fc41.aarch64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.aarch64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-5.fc41.aarch64 openssl-libs-3.2.2-9.fc42.aarch64 p11-kit-0.25.5-3.fc41.aarch64 p11-kit-trust-0.25.5-3.fc41.aarch64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-6.fc42.aarch64 pam-libs-1.6.1-6.fc42.aarch64 patch-2.7.6-25.fc41.aarch64 pcre2-10.44-1.fc41.1.aarch64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.aarch64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.aarch64 popt-1.19-7.fc41.aarch64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.15.0-1.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.aarch64 redhat-rpm-config-295-1.fc42.noarch rpm-4.19.94-1.fc42.aarch64 rpm-build-4.19.94-1.fc42.aarch64 rpm-build-libs-4.19.94-1.fc42.aarch64 rpm-libs-4.19.94-1.fc42.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.aarch64 setup-2.15.0-5.fc41.noarch shadow-utils-4.16.0-4.fc42.aarch64 sqlite-libs-3.46.0-4.fc41.aarch64 systemd-libs-256.5-1.fc42.aarch64 tar-1.35-4.fc41.aarch64 unzip-6.0-64.fc41.aarch64 util-linux-2.40.2-8.fc42.aarch64 util-linux-core-2.40.2-8.fc42.aarch64 which-2.21-42.fc41.aarch64 xxhash-libs-0.8.2-3.fc41.aarch64 xz-5.6.2-2.fc41.aarch64 xz-libs-5.6.2-2.fc41.aarch64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.aarch64 zlib-ng-compat-2.2.2-1.fc42.aarch64 zstd-1.5.6-2.fc41.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.1-2.fc42.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-aarch64-1727343304.927975/root/var/log’: No such file or directory INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1727343304.927975/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-6rdqc23s/python-pysam/python-pysam.spec) Config(child) 0 minutes 14 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-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727343304.927975/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727343304.927975/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-aarch64-1727343304.927975/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.aarch64 rpm-sequoia-1.7.0-2.fc41.aarch64 dnf5-5.2.6.2-1.fc42.aarch64 dnf5-plugins-5.2.6.2-1.fc42.aarch64 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: aarch64 Building for target aarch64 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% | 37.5 KiB/s | 1.5 KiB | 00m00s fedora 100% | 33.7 KiB/s | 7.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel aarch64 1.0.8-19.fc41 fedora 309.8 KiB gcc aarch64 14.2.1-3.fc42 fedora 93.8 MiB python3-cython aarch64 3.0.11-1.fc41 fedora 19.1 MiB python3-devel aarch64 3.13.0~rc2-3.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 2.0.0-6.fc41 fedora 317.9 KiB xz-devel aarch64 1:5.6.2-2.fc41 fedora 255.6 KiB zlib-ng-compat-devel aarch64 2.2.2-1.fc42 copr_base 106.8 KiB Installing dependencies: annobin-docs noarch 12.70-1.fc42 fedora 97.7 KiB annobin-plugin-gcc aarch64 12.70-1.fc42 fedora 1.1 MiB cmake-filesystem aarch64 3.28.3-7.fc41 fedora 0.0 B cpp aarch64 14.2.1-3.fc42 fedora 31.8 MiB expat aarch64 2.6.3-1.fc42 fedora 539.6 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 aarch64 14.2.1-3.fc42 fedora 197.1 KiB glibc-devel aarch64 2.40.9000-5.fc42 copr_base 2.2 MiB google-roboto-slab-fonts noarch 1.100263-0.24.20150923git.fc41 fedora 699.6 KiB kernel-headers aarch64 6.11.0-63.fc42 fedora 6.3 MiB lato-fonts noarch 2.015-22.fc41 fedora 11.3 MiB libasan aarch64 14.2.1-3.fc42 fedora 1.6 MiB libatomic aarch64 14.2.1-3.fc42 fedora 196.9 KiB libb2 aarch64 0.98.1-12.fc41 fedora 202.2 KiB libmpc aarch64 1.3.1-6.fc41 fedora 280.8 KiB libubsan aarch64 14.2.1-3.fc42 fedora 539.3 KiB libxcrypt-devel aarch64 4.4.36-7.fc41 fedora 30.3 KiB make aarch64 1:4.4.1-8.fc41 fedora 1.8 MiB mpdecimal aarch64 2.5.1-16.fc41 fedora 328.9 KiB pyproject-rpm-macros noarch 1.15.0-1.fc42 fedora 109.0 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 aarch64 3.13.0~rc2-3.fc42 fedora 211.8 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 0.20.1-6.fc41 fedora 4.8 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 aarch64 3.13.0~rc2-3.fc42 fedora 49.8 MiB python3-markupsafe aarch64 2.1.5-3.fc41 fedora 237.6 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: 51 packages Total size of inbound packages is 85 MiB. Need to download 17 MiB. After this operation, 298 MiB extra will be used (install 298 MiB, remove 0 B). [1/1] bzip2-devel-0:1.0.8-19.fc41.aarch 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] gcc-0:14.2.1-3.fc42.aarch64 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] python3-devel-0:3.13.0~rc2-3.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] python3-cython-0:3.0.11-1.fc41.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/6] python3-setuptools-0:69.2.0-8.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/8] xz-devel-1:5.6.2-2.fc41.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [4/9] zlib-ng-compat-devel-0:2.2.2-1.fc 100% | 0.0 B/s | 0.0 B 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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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.RCr07A + 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.nfCF0B + 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/libcvcf.c pysam/libcutils.c pysam/libctabixproxies.c pysam/libctabix.c pysam/libcsamtools.c pysam/libcsamfile.c pysam/libchtslib.c pysam/libcfaidx.c pysam/libcbgzf.c pysam/libcbcftools.c pysam/libcbcf.c pysam/libcalignmentfile.c pysam/libcalignedsegment.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.OhTLCy + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none 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... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none 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: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # 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-aarch64-cpython-313 creating build/lib.linux-aarch64-cpython-313/pysam copying pysam/config.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/version.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/utils.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/samtools.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/bcftools.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/__init__.py -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/Pileup.py -> build/lib.linux-aarch64-cpython-313/pysam creating build/lib.linux-aarch64-cpython-313/pysam/include copying pysam/include/__init__.py -> build/lib.linux-aarch64-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-aarch64-cpython-313/pysam copying pysam/csamtools_util.h -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/htslib_util.c -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/htslib_util.h -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcf.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcf.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcf.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libchtslib.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libchtslib.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libchtslib.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabix.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabix.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabix.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcutils.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcutils.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcutils.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcvcf.pxd -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcvcf.pyi -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/libcvcf.pyx -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/py.typed -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/pysam_stream.h -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/pysam_util.c -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/pysam_util.h -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/version.h -> build/lib.linux-aarch64-cpython-313/pysam copying pysam/version.pyi -> build/lib.linux-aarch64-cpython-313/pysam creating build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/README -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools creating build/lib.linux-aarch64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-aarch64-cpython-313/pysam/include/samtools creating build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/README -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-aarch64-cpython-313/pysam/include/bcftools creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/README -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/configure -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/header.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/header.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/region.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/cram creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/m4 creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib creating build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-aarch64-cpython-313/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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_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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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_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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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_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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-cpython-313 creating build/temp.linux-aarch64-cpython-313/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-313/pysam/htslib_util.o build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-aarch64-cpython-313/pysam/libchtslib.cpython-313-aarch64-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-aarch64-cpython-313/samtools creating build/temp.linux-aarch64-cpython-313/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-313/pysam/libcsamtools.o build/temp.linux-aarch64-cpython-313/samtools/amplicon_stats.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam2depth.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_addrprg.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_aux.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_cat.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_color.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_consensus.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_fastq.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_flags.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_import.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_index.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_lpileup.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_markdup.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_mate.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_md.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_plbuf.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_plcmd.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_quickcheck.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_reheader.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_rmdup.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_rmdupse.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_samples.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_sort.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_split.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bam_stat.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bamshuf.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bamtk.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bedcov.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/bedidx.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/consensus_pileup.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/coverage.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/cram_size.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/cut_target.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/dict.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/faidx.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/lz4/lz4.o build/temp.linux-aarch64-cpython-313/samtools/padding.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/phase.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/reference.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/reset.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/sam_opts.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/sam_utils.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/sam_view.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/sample.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/samtools.pysam.o build/temp.linux-aarch64-cpython-313/samtools/stats.c.pysam.o build/temp.linux-aarch64-cpython-313/samtools/stats_isize.c.pysam.o build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcsamtools.cpython-313-aarch64-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-aarch64-cpython-313/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-313/bcftools/HMM.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/abuf.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bam2bcf.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bam_sample.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bcftools.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/bin.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/ccall.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/cols.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/consensus.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/convert.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/csq.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/dist.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/em.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/extsort.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/filter.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/gff.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/gvcf.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/hclust.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/kmin.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/main.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/mcall.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/mpileup.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/ploidy.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/prob1.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/read_consensus.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/regidx.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/reheader.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/smpl_ilist.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/str_finder.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/tabix.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/tsv2vcf.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfannotate.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfbuf.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfcall.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfcnv.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfconcat.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfconvert.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcffilter.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfhead.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfindex.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfisec.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfmerge.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfnorm.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfplugin.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfquery.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfroh.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfsom.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfsort.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfstats.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcfview.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/vcmp.c.pysam.o build/temp.linux-aarch64-cpython-313/bcftools/version.c.pysam.o build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcbcftools.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-313/pysam/libcutils.o build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcsamtools.cpython-313-aarch64-linux-gnu -lcbcftools.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcutils.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcalignmentfile.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcsamfile.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcalignedsegment.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libctabix.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcfaidx.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcbcf.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcbgzf.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libctabixproxies.cpython-313-aarch64-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 -fexceptions -fexceptions -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-aarch64-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-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-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -Lbuild/lib.linux-aarch64-cpython-313/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-313-aarch64-linux-gnu -lcutils.cpython-313-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/pysam/libcvcf.cpython-313-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/build/lib.linux-aarch64-cpython-313 + PYTHONPATH=/builddir/build/BUILD/python-pysam-0.22.1-build/pysam-0.22.1/build/lib.linux-aarch64-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.UFYAwx + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none 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... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none 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= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # 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 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-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__ copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-cpython-313/pysam/libcvcf.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libctabixproxies.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcbgzf.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcbcf.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcfaidx.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libctabix.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcalignedsegment.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcsamfile.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcalignmentfile.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcutils.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcbcftools.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libcsamtools.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-cpython-313/pysam/libchtslib.cpython-313-aarch64-linux-gnu.so -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-cpython-313/pysam/cbcftools_util.h -> /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 creating /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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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/os copying build/lib.linux-aarch64-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-aarch64-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 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-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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 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-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 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-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 creating /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-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/samtools/lz4 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-cpython-313/pysam/include/__init__.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/include copying build/lib.linux-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-cpython-313/pysam/config.py -> /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam 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 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 writing byte-compilation script '/tmp/tmp4rvzzwvo.py' /usr/bin/python3 /tmp/tmp4rvzzwvo.py removing /tmp/tmp4rvzzwvo.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 -j4 --strict-build-id -m -i --build-id-seed 0.22.1-2.fc42 --unique-debug-suffix -0.22.1-2.fc42.aarch64 --unique-debug-src-base python-pysam-0.22.1-2.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -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.aarch64 53729 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 -j4 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /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.opt-1.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.opt-1.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.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/samtools.cpython-313.opt-1.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.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.22.1-build/BUILDROOT/usr/lib64/python3.13/site-packages/pysam/__pycache__/__init__.cpython-313.opt-1.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.opt-1.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__/Pileup.cpython-313.pyc: replacing with normalized version Scanned 40 directories and 786 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.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.mn8FL4 + 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.blLDid + 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-aarch64-linux-gnu.so()(64bit) libcalignmentfile.cpython-313-aarch64-linux-gnu.so()(64bit) libcbcf.cpython-313-aarch64-linux-gnu.so()(64bit) libcbcftools.cpython-313-aarch64-linux-gnu.so()(64bit) libcbgzf.cpython-313-aarch64-linux-gnu.so()(64bit) libcfaidx.cpython-313-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-313-aarch64-linux-gnu.so()(64bit) libcsamfile.cpython-313-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-313-aarch64-linux-gnu.so()(64bit) libctabix.cpython-313-aarch64-linux-gnu.so()(64bit) libctabixproxies.cpython-313-aarch64-linux-gnu.so()(64bit) libcutils.cpython-313-aarch64-linux-gnu.so()(64bit) libcvcf.cpython-313-aarch64-linux-gnu.so()(64bit) python-pysam = 0.22.1-2.fc42 python3-pysam = 0.22.1-2.fc42 python3-pysam(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_ABI_DT_RELR)(64bit) libcbcftools.cpython-313-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-313-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-313-aarch64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(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.aarch64 Provides: python-pysam-devel = 0.22.1-2.fc42 python3-pysam-devel = 0.22.1-2.fc42 python3-pysam-devel(aarch-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.B86nWK + 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.aarch64 Provides: python-pysam-debugsource = 0.22.1-2.fc42 python-pysam-debugsource(aarch-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.aarch64 Provides: debuginfo(build-id) = 215c6bc4b53f779dec9f175c9c631cb5448d3f2a debuginfo(build-id) = 38f19cf45f927644f30cd6ceffe476ef6d95a80f debuginfo(build-id) = 46ba7ac9b77a68f06f50960149d6ba8227ee1c2a debuginfo(build-id) = 79ad4d36f00565dab0337ff8b21694b62291fef8 debuginfo(build-id) = 8d50274610751fc4c280339ae6055e3515d7e8ea debuginfo(build-id) = a01eaa3577d0a353e014ae1fa9693dc8534f3fff debuginfo(build-id) = c02f1aa2f4c57c02d4237c7bc4ab4b80007c0277 debuginfo(build-id) = c3b47578b0455524979c5953456b39a6b18e7756 debuginfo(build-id) = d58dfe3cba8f38acf627d3a7368af2e2f42d3439 debuginfo(build-id) = e4807cc83e9b240b1d703f08c18315045546ebb4 debuginfo(build-id) = eae7ff082df6682029ff28ed585d1eb38648a3a2 debuginfo(build-id) = efc3d61e5f09498fd8896e197bde038a9c1c46e4 debuginfo(build-id) = f0ec85c6e71feafb8a8c7d33ecb97589e9ede9a8 libcalignedsegment.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcalignmentfile.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcbcf.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcbcftools.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcbgzf.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcfaidx.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libchtslib.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcsamfile.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcsamtools.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libctabix.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libctabixproxies.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcutils.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) libcvcf.cpython-313-aarch64-linux-gnu.so-0.22.1-2.fc42.aarch64.debug()(64bit) python-pysam-debuginfo = 0.22.1-2.fc42 python3-pysam-debuginfo = 0.22.1-2.fc42 python3-pysam-debuginfo(aarch-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(aarch-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-0.22.1-2.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.1-2.fc42.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.1-2.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.1-2.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.1-2.fc42.aarch64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.1azxGc + 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-aarch64-1727343304.927975/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 16 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", "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": "aarch64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "aarch64" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "aarch64" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "aarch64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.22.1", "release": "2.fc42", "arch": "noarch" } ] } RPMResults finished