Warning: Permanently added '18.208.190.54' (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/10439516-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64 Version: 1.8 PID: 12927 Logging PID: 12929 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10439516, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'a96a3d64dce1964a33ca88588668aed629a3ab15', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/davidsch/testa/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.24.0-1', 'project_dirname': 'testa', 'project_name': 'testa', 'project_owner': 'davidsch', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/davidsch/testa/fedora-rawhide-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'davidsch/testa--davidsch', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'davidsch', 'tags': [], 'task_id': '10439516-fedora-rawhide-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/davidsch/testa/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/davidsch/testa/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam'... Running: git checkout a96a3d64dce1964a33ca88588668aed629a3ab15 -- cmd: ['git', 'checkout', 'a96a3d64dce1964a33ca88588668aed629a3ab15', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam rc: 0 stdout: stderr: Note: switching to 'a96a3d64dce1964a33ca88588668aed629a3ab15'. 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 a96a3d6 automatic import of python-pysam Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/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-0.24.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o pysam-0.24.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/davidsch/testa/python-pysam/pysam-0.24.0.tar.gz/md5/5ee49a21895c2a5b7b8731c181296267/pysam-0.24.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 5079k 100 5079k 0 0 137M 0 --:--:-- --:--:-- --:--:-- 137M INFO: Reading stdout from command: md5sum pysam-0.24.0.tar.gz tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1778317779.858557 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.7 starting (python version = 3.14.2, NVR = mock-6.7-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1778317779.858557 -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-blo3kfh8/python-pysam/python-pysam.spec) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 6.7 INFO: Mock Version: 6.7 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1778317779.858557/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-3f4966be-0dd3-46cf-8612-7ed77de99fb1 INFO: Checking that 3e29b2f2dc8e63f125edcdb123c52a6a74dcdbe04bb6c0439e52e18c70e14a86 image matches host's architecture INFO: Copy content of container 3e29b2f2dc8e63f125edcdb123c52a6a74dcdbe04bb6c0439e52e18c70e14a86 to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1778317779.858557/root INFO: mounting 3e29b2f2dc8e63f125edcdb123c52a6a74dcdbe04bb6c0439e52e18c70e14a86 with podman image mount INFO: image 3e29b2f2dc8e63f125edcdb123c52a6a74dcdbe04bb6c0439e52e18c70e14a86 as /var/lib/containers/storage/overlay/87df1094afcacf007c4f9174d97c24ed76abcfac9257a92eea3d6967acbe8909/merged INFO: umounting image 3e29b2f2dc8e63f125edcdb123c52a6a74dcdbe04bb6c0439e52e18c70e14a86 (/var/lib/containers/storage/overlay/87df1094afcacf007c4f9174d97c24ed76abcfac9257a92eea3d6967acbe8909/merged) with podman image umount INFO: Removing image mock-bootstrap-3f4966be-0dd3-46cf-8612-7ed77de99fb1 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-aarch64-1778317779.858557/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-5.fc45.aarch64 rpm-sequoia-1.10.2-1.fc45.aarch64 dnf5-5.4.2.0-1.fc45.aarch64 dnf5-plugins-5.4.2.0-1.fc45.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 286.1 KiB/s | 8.3 KiB | 00m00s fedora 100% | 31.1 MiB/s | 20.7 MiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 0:5.3.9-3.fc44 fedora 8.4 MiB bzip2 aarch64 0:1.0.8-23.fc44 fedora 171.1 KiB coreutils aarch64 0:9.11-1.fc45 fedora 8.6 MiB cpio aarch64 0:2.15-9.fc44 fedora 1.1 MiB diffutils aarch64 0:3.12-5.fc44 fedora 1.6 MiB fedora-release-common noarch 0:45-0.7 fedora 4.2 KiB findutils aarch64 1:4.10.0-7.fc44 fedora 1.9 MiB gawk aarch64 0:5.4.0-2.fc45 fedora 2.9 MiB glibc-minimal-langpack aarch64 0:2.43.9000-14.fc45 fedora 0.0 B grep aarch64 0:3.12-3.fc44 fedora 1.0 MiB gzip aarch64 0:1.14-2.fc44 fedora 437.5 KiB info aarch64 0:7.3-1.fc45 fedora 424.3 KiB patch aarch64 0:2.8-4.fc44 fedora 262.4 KiB redhat-rpm-config noarch 0:344-1.fc45 fedora 183.7 KiB rpm-build aarch64 0:6.0.1-5.fc45 fedora 597.8 KiB sed aarch64 0:4.10-1.fc45 fedora 943.4 KiB shadow-utils aarch64 2:4.19.3-2.fc45 fedora 4.4 MiB tar aarch64 2:1.35-8.fc44 fedora 3.0 MiB unzip aarch64 0:6.0-69.fc44 fedora 533.8 KiB util-linux aarch64 0:2.42-7.fc45 fedora 6.9 MiB which aarch64 0:2.23-4.fc44 fedora 123.3 KiB xz aarch64 1:5.8.3-1.fc45 fedora 1.5 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-2.fc45 fedora 3.5 KiB add-determinism aarch64 0:0.7.3-2.fc45 fedora 2.0 MiB alternatives aarch64 0:1.33-5.fc44 fedora 90.1 KiB ansible-srpm-macros noarch 0:1-20.1.fc44 fedora 35.7 KiB audit-libs aarch64 0:4.1.4-1.fc45 fedora 486.7 KiB binutils aarch64 0:2.46.50-7.fc45 fedora 31.5 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-2.fc45 fedora 1.2 KiB bzip2-libs aarch64 0:1.0.8-23.fc44 fedora 72.5 KiB ca-certificates noarch 0:2025.2.80_v9.0.304-7.fc45 fedora 2.7 MiB cmake-srpm-macros noarch 0:4.3.0-1.fc45 fedora 524.0 B coreutils-common aarch64 0:9.11-1.fc45 fedora 10.9 MiB crypto-policies noarch 0:20251128-3.git19878fe.fc44 fedora 132.6 KiB curl aarch64 0:8.20.0~rc3-1.fc45 fedora 463.1 KiB cyrus-sasl-lib aarch64 0:2.1.28-35.fc44 fedora 2.4 MiB debugedit aarch64 0:5.3-2.fc45 fedora 320.9 KiB dwz aarch64 0:0.16-3.fc44 fedora 322.4 KiB ed aarch64 0:1.22.5-2.fc45 fedora 157.7 KiB efi-srpm-macros noarch 0:6-6.fc44 fedora 40.2 KiB elfutils aarch64 0:0.195-1.fc45 fedora 3.6 MiB elfutils-debuginfod-client aarch64 0:0.195-1.fc45 fedora 143.9 KiB elfutils-libelf aarch64 0:0.195-1.fc45 fedora 1.2 MiB elfutils-libs aarch64 0:0.195-1.fc45 fedora 746.5 KiB erlang-srpm-macros noarch 0:0.3.11-1.fc45 fedora 1.9 KiB fedora-gpg-keys noarch 0:45-0.1 fedora 133.4 KiB fedora-release noarch 0:45-0.7 fedora 0.0 B fedora-release-identity-basic noarch 0:45-0.7 fedora 664.0 B fedora-repos noarch 0:45-0.1 fedora 4.9 KiB fedora-repos-rawhide noarch 0:45-0.1 fedora 2.2 KiB file aarch64 0:5.47-2.fc45 fedora 141.2 KiB file-libs aarch64 0:5.47-2.fc45 fedora 12.2 MiB filesystem aarch64 0:3.18-56.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-56.fc45 fedora 38.2 KiB fonts-srpm-macros noarch 1:5.0.0-3.fc45 fedora 55.8 KiB forge-srpm-macros noarch 0:0.4.0-4.fc44 fedora 38.9 KiB fpc-srpm-macros noarch 0:1.3-16.fc44 fedora 144.0 B gap-srpm-macros noarch 0:2-2.fc44 fedora 2.1 KiB gdb-minimal aarch64 0:17.1-5.fc45 fedora 13.5 MiB gdbm-libs aarch64 1:1.23-11.fc44 fedora 233.7 KiB ghc-srpm-macros noarch 0:1.10-1.fc44 fedora 792.0 B glibc aarch64 0:2.43.9000-14.fc45 fedora 6.4 MiB glibc-common aarch64 0:2.43.9000-14.fc45 fedora 1.3 MiB glibc-gconv-extra aarch64 0:2.43.9000-14.fc45 fedora 18.6 MiB gmp aarch64 1:6.3.0-5.fc44 fedora 657.9 KiB gnat-srpm-macros noarch 0:7-2.fc44 fedora 1.0 KiB gnulib-l10n noarch 0:20241231-2.fc44 fedora 655.0 KiB gnupg2 aarch64 0:2.4.9-7.fc45 fedora 6.4 MiB gnupg2-dirmngr aarch64 0:2.4.9-7.fc45 fedora 646.2 KiB gnupg2-gpg-agent aarch64 0:2.4.9-7.fc45 fedora 846.9 KiB gnupg2-gpgconf aarch64 0:2.4.9-7.fc45 fedora 321.8 KiB gnupg2-keyboxd aarch64 0:2.4.9-7.fc45 fedora 233.2 KiB gnupg2-verify aarch64 0:2.4.9-7.fc45 fedora 364.3 KiB gnutls aarch64 0:3.8.13-1.fc45 fedora 3.7 MiB go-srpm-macros noarch 0:3.8.0-2.fc44 fedora 61.9 KiB gpgverify noarch 0:2.2-4.fc44 fedora 8.7 KiB ima-evm-utils-libs aarch64 0:1.6.2-10.fc45 fedora 92.6 KiB jansson aarch64 0:2.14-4.fc44 fedora 93.0 KiB java-srpm-macros noarch 0:1-8.fc44 fedora 870.0 B json-c aarch64 0:0.18-8.fc44 fedora 138.5 KiB kernel-srpm-macros noarch 0:1.0-29.fc45 fedora 1.9 KiB keyutils-libs aarch64 0:1.6.3-7.fc44 fedora 98.2 KiB krb5-libs aarch64 0:1.22.2-7.fc45 fedora 2.5 MiB libacl aarch64 0:2.3.2-6.fc44 fedora 67.8 KiB libarchive aarch64 0:3.8.7-1.fc45 fedora 975.6 KiB libassuan aarch64 0:2.5.7-5.fc44 fedora 215.8 KiB libattr aarch64 0:2.5.2-8.fc44 fedora 68.3 KiB libblkid aarch64 0:2.42-7.fc45 fedora 290.3 KiB libbrotli aarch64 0:1.2.0-3.fc44 fedora 909.1 KiB libcap aarch64 0:2.78-1.fc45 fedora 508.4 KiB libcap-ng aarch64 0:0.9.3-1.fc45 fedora 160.9 KiB libcbor aarch64 0:0.14.0-2.fc45 fedora 139.6 KiB libcom_err aarch64 0:1.47.4-1.fc45 fedora 111.1 KiB libcurl aarch64 0:8.20.0~rc3-1.fc45 fedora 981.6 KiB libeconf aarch64 0:0.7.9-3.fc44 fedora 80.8 KiB libevent aarch64 0:2.1.12-17.fc44 fedora 1.1 MiB libfdisk aarch64 0:2.42-7.fc45 fedora 418.8 KiB libffi aarch64 0:3.5.2-2.fc44 fedora 155.7 KiB libfido2 aarch64 0:1.17.0-2.fc45 fedora 280.7 KiB libfsverity aarch64 0:1.7-1.fc45 fedora 68.3 KiB libgcc aarch64 0:16.1.1-1.fc45 fedora 222.3 KiB libgcrypt aarch64 0:1.12.2-1.fc45 fedora 1.2 MiB libgomp aarch64 0:16.1.1-1.fc45 fedora 592.8 KiB libgpg-error aarch64 0:1.60-1.fc45 fedora 996.8 KiB libidn2 aarch64 0:2.3.8-3.fc44 fedora 560.4 KiB libksba aarch64 0:1.6.8-1.fc45 fedora 401.7 KiB liblastlog2 aarch64 0:2.42-7.fc45 fedora 137.7 KiB libmount aarch64 0:2.42-7.fc45 fedora 420.2 KiB libnghttp2 aarch64 0:1.69.0-1.fc45 fedora 197.9 KiB libnghttp3 aarch64 0:1.15.0-1.fc44 fedora 206.6 KiB libpkgconf aarch64 0:2.5.1-1.fc45 fedora 133.9 KiB libpsl aarch64 0:0.21.5-7.fc44 fedora 132.3 KiB libselinux aarch64 0:3.10-1.fc44 fedora 201.0 KiB libselinux-utils aarch64 0:3.10-1.fc44 fedora 1.3 MiB libsemanage aarch64 0:3.10-1.fc44 fedora 360.0 KiB libsepol aarch64 0:3.10-1.fc44 fedora 810.0 KiB libsmartcols aarch64 0:2.42-7.fc45 fedora 224.4 KiB libssh aarch64 0:0.12.0-1.fc45 fedora 718.9 KiB libssh-config noarch 0:0.12.0-1.fc45 fedora 277.0 B libstdc++ aarch64 0:16.1.1-1.fc45 fedora 3.0 MiB libtasn1 aarch64 0:4.21.0-1.fc45 fedora 220.7 KiB libtool-ltdl aarch64 0:2.5.4-10.fc44 fedora 93.9 KiB libunistring aarch64 0:1.1-11.fc44 fedora 1.7 MiB libusb1 aarch64 0:1.0.29-5.fc44 fedora 178.8 KiB libuuid aarch64 0:2.42-7.fc45 fedora 69.3 KiB libverto aarch64 0:0.3.2-12.fc44 fedora 69.3 KiB libxcrypt aarch64 0:4.5.2-3.fc44 fedora 273.2 KiB libxml2 aarch64 0:2.12.10-6.fc44 fedora 1.9 MiB libzstd aarch64 0:1.5.7-5.fc44 fedora 860.2 KiB linkdupes aarch64 0:0.7.3-2.fc45 fedora 713.7 KiB lua-libs aarch64 0:5.5.0-1.fc45 fedora 329.9 KiB lua-srpm-macros noarch 0:1-17.fc44 fedora 1.3 KiB lz4-libs aarch64 0:1.10.0-4.fc44 fedora 197.3 KiB mpfr aarch64 0:4.2.2-3.fc44 fedora 755.4 KiB ncurses-base noarch 0:6.6-2.fc45 fedora 329.7 KiB ncurses-libs aarch64 0:6.6-2.fc45 fedora 1.2 MiB nettle aarch64 0:3.10.1-3.fc44 fedora 765.0 KiB ngtcp2 aarch64 0:1.22.1-1.fc45 fedora 341.1 KiB ngtcp2-crypto-ossl aarch64 0:1.22.1-1.fc45 fedora 67.5 KiB npth aarch64 0:1.8-4.fc44 fedora 93.3 KiB ocaml-srpm-macros noarch 0:11-3.fc44 fedora 1.9 KiB openblas-srpm-macros noarch 0:2-21.fc44 fedora 112.0 B openldap aarch64 0:2.6.13-1.fc45 fedora 764.2 KiB openssl-libs aarch64 1:3.5.6-1.fc45 fedora 7.4 MiB p11-kit aarch64 0:0.26.2-1.fc45 fedora 2.7 MiB p11-kit-trust aarch64 0:0.26.2-1.fc45 fedora 530.1 KiB package-notes-srpm-macros noarch 0:0.17-3.fc45 fedora 1.6 KiB pam-libs aarch64 0:1.7.2-1.fc44 fedora 222.6 KiB pcre2 aarch64 0:10.47-1.fc44.1 fedora 714.3 KiB pcre2-syntax noarch 0:10.47-1.fc44.1 fedora 281.9 KiB perl-srpm-macros noarch 0:1-61.fc44 fedora 861.0 B pkgconf aarch64 0:2.5.1-1.fc45 fedora 116.7 KiB pkgconf-m4 noarch 0:2.5.1-1.fc45 fedora 14.3 KiB pkgconf-pkg-config aarch64 0:2.5.1-1.fc45 fedora 990.0 B policycoreutils aarch64 0:3.10-3.fc45 fedora 1.5 MiB popt aarch64 0:1.19-10.fc44 fedora 144.6 KiB publicsuffix-list-dafsa noarch 0:20260116-1.fc44 fedora 70.4 KiB pyproject-srpm-macros noarch 0:1.22.0-1.fc45 fedora 3.2 KiB python-srpm-macros noarch 0:3.14-12.fc45 fedora 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-2.fc44 fedora 500.0 B qt6-srpm-macros noarch 0:6.11.0-1.fc45 fedora 472.0 B readline aarch64 0:8.3-4.fc44 fedora 563.5 KiB redhat-systemd-presets noarch 0:102-1.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-1.fc45 fedora 16.6 KiB rpm aarch64 0:6.0.1-5.fc45 fedora 3.3 MiB rpm-build-libs aarch64 0:6.0.1-5.fc45 fedora 264.0 KiB rpm-libs aarch64 0:6.0.1-5.fc45 fedora 994.9 KiB rpm-plugin-selinux aarch64 0:6.0.1-5.fc45 fedora 67.8 KiB rpm-sequoia aarch64 0:1.10.2-1.fc45 fedora 2.2 MiB rpm-sign-libs aarch64 0:6.0.1-5.fc45 fedora 67.6 KiB rust-srpm-macros noarch 0:28.4-3.fc44 fedora 5.5 KiB selinux-policy noarch 0:45.2-1.fc45 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.2-1.fc45 fedora 18.6 MiB setup noarch 0:2.15.0-29.fc45 fedora 724.9 KiB sqlite-libs aarch64 0:3.53.0-1.fc45 fedora 1.6 MiB systemd-libs aarch64 0:260.1-2.fc45 fedora 2.5 MiB systemd-standalone-sysusers aarch64 0:260.1-2.fc45 fedora 847.9 KiB tpm2-tss aarch64 0:4.1.3-9.fc44 fedora 2.1 MiB tree-sitter-srpm-macros noarch 0:0.4.3-1.fc45 fedora 8.2 KiB util-linux-core aarch64 0:2.42-7.fc45 fedora 2.5 MiB xxhash-libs aarch64 0:0.8.3-4.fc44 fedora 85.8 KiB xz-libs aarch64 1:5.8.3-1.fc45 fedora 265.5 KiB zig-srpm-macros noarch 0:1-8.fc44 fedora 1.3 KiB zip aarch64 0:3.0-45.fc44 fedora 762.0 KiB zlib-ng-compat aarch64 0:2.3.3-5.fc45 fedora 133.3 KiB zstd aarch64 0:1.5.7-5.fc44 fedora 562.2 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 186 packages Total size of inbound packages is 68 MiB. Need to download 68 MiB. After this operation, 253 MiB extra will be used (install 253 MiB, remove 0 B). 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85.2 MiB/s | 174.6 KiB | 00m00s [155/186] libunistring-0:1.1-11.fc44.aa 100% | 175.2 MiB/s | 538.3 KiB | 00m00s [156/186] nettle-0:3.10.1-3.fc44.aarch6 100% | 103.9 MiB/s | 425.5 KiB | 00m00s [157/186] cyrus-sasl-lib-0:2.1.28-35.fc 100% | 151.0 MiB/s | 772.9 KiB | 00m00s [158/186] libevent-0:2.1.12-17.fc44.aar 100% | 66.0 MiB/s | 270.5 KiB | 00m00s [159/186] libtool-ltdl-0:2.5.4-10.fc44. 100% | 11.6 MiB/s | 35.6 KiB | 00m00s [160/186] gdbm-libs-1:1.23-11.fc44.aarc 100% | 55.0 MiB/s | 56.3 KiB | 00m00s [161/186] fedora-release-0:45-0.7.noarc 100% | 12.4 MiB/s | 12.7 KiB | 00m00s [162/186] systemd-standalone-sysusers-0 100% | 163.0 MiB/s | 333.8 KiB | 00m00s [163/186] xxhash-libs-0:0.8.3-4.fc44.aa 100% | 4.2 MiB/s | 34.5 KiB | 00m00s [164/186] gdb-minimal-0:17.1-5.fc45.aar 100% | 309.7 MiB/s | 4.3 MiB | 00m00s [165/186] fedora-release-identity-basic 100% | 1.1 MiB/s | 13.4 KiB | 00m00s [166/186] libcurl-0:8.20.0~rc3-1.fc45.a 100% | 70.5 MiB/s | 433.4 KiB | 00m00s [167/186] krb5-libs-0:1.22.2-7.fc45.aar 100% | 248.1 MiB/s | 762.1 KiB | 00m00s [168/186] libbrotli-0:1.2.0-3.fc44.aarc 100% | 85.1 MiB/s | 348.7 KiB | 00m00s [169/186] libnghttp2-0:1.69.0-1.fc45.aa 100% | 18.2 MiB/s | 74.4 KiB | 00m00s [170/186] libnghttp3-0:1.15.0-1.fc44.aa 100% | 67.2 MiB/s | 68.8 KiB | 00m00s [171/186] libpsl-0:0.21.5-7.fc44.aarch6 100% | 63.4 MiB/s | 64.9 KiB | 00m00s [172/186] libssh-0:0.12.0-1.fc45.aarch6 100% | 134.2 MiB/s | 274.8 KiB | 00m00s [173/186] ngtcp2-0:1.22.1-1.fc45.aarch6 100% | 71.9 MiB/s | 147.2 KiB | 00m00s [174/186] ngtcp2-crypto-ossl-0:1.22.1-1 100% | 12.7 MiB/s | 26.0 KiB | 00m00s [175/186] keyutils-libs-0:1.6.3-7.fc44. 100% | 30.7 MiB/s | 31.5 KiB | 00m00s [176/186] libcom_err-0:1.47.4-1.fc45.aa 100% | 26.0 MiB/s | 26.7 KiB | 00m00s [177/186] libverto-0:0.3.2-12.fc44.aarc 100% | 20.0 MiB/s | 20.5 KiB | 00m00s [178/186] publicsuffix-list-dafsa-0:202 100% | 58.9 MiB/s | 60.3 KiB | 00m00s [179/186] libfido2-0:1.17.0-2.fc45.aarc 100% | 96.6 MiB/s | 98.9 KiB | 00m00s [180/186] libssh-config-0:0.12.0-1.fc45 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [181/186] libcbor-0:0.14.0-2.fc45.aarch 100% | 34.2 MiB/s | 35.0 KiB | 00m00s [182/186] policycoreutils-0:3.10-3.fc45 100% | 85.6 MiB/s | 262.8 KiB | 00m00s [183/186] selinux-policy-0:45.2-1.fc45. 100% | 24.0 MiB/s | 73.8 KiB | 00m00s [184/186] libselinux-utils-0:3.10-1.fc4 100% | 59.7 MiB/s | 122.2 KiB | 00m00s [185/186] rpm-plugin-selinux-0:6.0.1-5. 100% | 4.7 MiB/s | 19.2 KiB | 00m00s [186/186] selinux-policy-targeted-0:45. 100% | 162.5 MiB/s | 6.8 MiB | 00m00s -------------------------------------------------------------------------------- [186/186] Total 100% | 215.1 MiB/s | 67.8 MiB | 00m00s Running transaction Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. [ 1/188] Verify package files 100% | 738.0 B/s | 186.0 B | 00m00s [ 2/188] Prepare transaction 100% | 2.2 KiB/s | 186.0 B | 00m00s [ 3/188] Installing libgcc-0:16.1.1-1. 100% | 109.4 MiB/s | 224.0 KiB | 00m00s [ 4/188] Installing redhat-systemd-pre 100% | 0.0 B/s | 1.5 KiB | 00m00s [ 5/188] Installing redhat-systemd-pre 100% | 0.0 B/s | 17.8 KiB | 00m00s [ 6/188] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 7/188] Installing publicsuffix-list- 100% | 69.4 MiB/s | 71.1 KiB | 00m00s [ 8/188] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0 B | 00m00s [ 9/188] Installing fedora-gpg-keys-0: 100% | 29.6 MiB/s | 182.1 KiB | 00m00s [ 10/188] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 11/188] Installing fedora-repos-0:45- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 12/188] Installing fedora-release-com 100% | 7.3 MiB/s | 7.4 KiB | 00m00s [ 13/188] Installing fedora-release-0:4 100% | 20.2 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-29.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-29.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/188] Installing setup-0:2.15.0-29. 100% | 29.7 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/188] Installing filesystem-0:3.18- 100% | 1.9 MiB/s | 289.4 KiB | 00m00s [ 16/188] Installing pkgconf-m4-0:2.5.1 100% | 14.4 MiB/s | 14.7 KiB | 00m00s [ 17/188] Installing pcre2-syntax-0:10. 100% | 138.8 MiB/s | 284.3 KiB | 00m00s [ 18/188] Installing gnulib-l10n-0:2024 100% | 129.3 MiB/s | 661.9 KiB | 00m00s [ 19/188] Installing coreutils-common-0 100% | 313.1 MiB/s | 11.0 MiB | 00m00s [ 20/188] Installing ncurses-base-0:6.6 100% | 57.8 MiB/s | 355.3 KiB | 00m00s [ 21/188] Installing bash-0:5.3.9-3.fc4 100% | 183.3 MiB/s | 8.4 MiB | 00m00s [ 22/188] Installing glibc-common-0:2.4 100% | 45.8 MiB/s | 1.3 MiB | 00m00s [ 23/188] Installing glibc-gconv-extra- 100% | 397.5 MiB/s | 18.7 MiB | 00m00s [ 24/188] Installing glibc-0:2.43.9000- 100% | 131.8 MiB/s | 6.5 MiB | 00m00s [ 25/188] Installing ncurses-libs-0:6.6 100% | 249.1 MiB/s | 1.2 MiB | 00m00s [ 26/188] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 27/188] Installing zlib-ng-compat-0:2 100% | 131.0 MiB/s | 134.1 KiB | 00m00s [ 28/188] Installing bzip2-libs-0:1.0.8 100% | 71.9 MiB/s | 73.6 KiB | 00m00s [ 29/188] Installing libgpg-error-0:1.6 100% | 36.3 MiB/s | 1.0 MiB | 00m00s [ 30/188] Installing libstdc++-0:16.1.1 100% | 330.1 MiB/s | 3.0 MiB | 00m00s [ 31/188] Installing libassuan-0:2.5.7- 100% | 212.6 MiB/s | 217.7 KiB | 00m00s [ 32/188] Installing libgcrypt-0:1.12.2 100% | 240.0 MiB/s | 1.2 MiB | 00m00s [ 33/188] Installing readline-0:8.3-4.f 100% | 276.2 MiB/s | 565.6 KiB | 00m00s [ 34/188] Installing gmp-1:6.3.0-5.fc44 100% | 214.9 MiB/s | 660.1 KiB | 00m00s [ 35/188] Installing systemd-libs-0:260 100% | 315.9 MiB/s | 2.5 MiB | 00m00s [ 36/188] Installing libuuid-0:2.42-7.f 100% | 68.7 MiB/s | 70.3 KiB | 00m00s [ 37/188] Installing xz-libs-1:5.8.3-1. 100% | 260.3 MiB/s | 266.6 KiB | 00m00s [ 38/188] Installing libzstd-0:1.5.7-5. 100% | 280.4 MiB/s | 861.5 KiB | 00m00s [ 39/188] Installing elfutils-libelf-0: 100% | 294.4 MiB/s | 1.2 MiB | 00m00s [ 40/188] Installing popt-0:1.19-10.fc4 100% | 36.9 MiB/s | 151.3 KiB | 00m00s [ 41/188] Installing npth-0:1.8-4.fc44. 100% | 92.2 MiB/s | 94.4 KiB | 00m00s [ 42/188] Installing elfutils-libs-0:0. 100% | 243.6 MiB/s | 748.4 KiB | 00m00s [ 43/188] Installing libblkid-0:2.42-7. 100% | 284.6 MiB/s | 291.4 KiB | 00m00s [ 44/188] Installing libattr-0:2.5.2-8. 100% | 67.6 MiB/s | 69.3 KiB | 00m00s [ 45/188] Installing libacl-0:2.3.2-6.f 100% | 67.0 MiB/s | 68.6 KiB | 00m00s [ 46/188] Installing libsepol-0:3.10-1. 100% | 264.0 MiB/s | 810.9 KiB | 00m00s [ 47/188] Installing sqlite-libs-0:3.53 100% | 261.4 MiB/s | 1.6 MiB | 00m00s [ 48/188] Installing gnupg2-gpgconf-0:2 100% | 13.2 MiB/s | 323.9 KiB | 00m00s [ 49/188] Installing pcre2-0:10.47-1.fc 100% | 233.0 MiB/s | 715.7 KiB | 00m00s [ 50/188] Installing libselinux-0:3.10- 100% | 197.5 MiB/s | 202.2 KiB | 00m00s [ 51/188] Installing grep-0:3.12-3.fc44 100% | 35.8 MiB/s | 1.0 MiB | 00m00s [ 52/188] Installing sed-0:4.10-1.fc45. 100% | 32.1 MiB/s | 951.9 KiB | 00m00s [ 53/188] Installing findutils-1:4.10.0 100% | 64.0 MiB/s | 1.9 MiB | 00m00s [ 54/188] Installing libxcrypt-0:4.5.2- 100% | 134.7 MiB/s | 275.9 KiB | 00m00s [ 55/188] Installing libtasn1-0:4.21.0- 100% | 217.3 MiB/s | 222.5 KiB | 00m00s [ 56/188] Installing libunistring-0:1.1 100% | 291.0 MiB/s | 1.7 MiB | 00m00s [ 57/188] Installing libidn2-0:2.3.8-3. 100% | 61.5 MiB/s | 566.6 KiB | 00m00s [ 58/188] Installing crypto-policies-0: 100% | 22.0 MiB/s | 157.7 KiB | 00m00s [ 59/188] Installing xz-1:5.8.3-1.fc45. 100% | 47.8 MiB/s | 1.5 MiB | 00m00s [ 60/188] Installing libmount-0:2.42-7. 100% | 205.7 MiB/s | 421.3 KiB | 00m00s [ 61/188] Installing gnupg2-verify-0:2. 100% | 14.9 MiB/s | 365.7 KiB | 00m00s [ 62/188] Installing dwz-0:0.16-3.fc44. 100% | 13.2 MiB/s | 323.8 KiB | 00m00s [ 63/188] Installing mpfr-0:4.2.2-3.fc4 100% | 184.8 MiB/s | 757.1 KiB | 00m00s [ 64/188] Installing gawk-0:5.4.0-2.fc4 100% | 93.9 MiB/s | 2.9 MiB | 00m00s [ 65/188] Installing libksba-0:1.6.8-1. 100% | 197.4 MiB/s | 404.3 KiB | 00m00s [ 66/188] Installing unzip-0:6.0-69.fc4 100% | 21.0 MiB/s | 537.3 KiB | 00m00s [ 67/188] Installing file-libs-0:5.47-2 100% | 610.3 MiB/s | 12.2 MiB | 00m00s [ 68/188] Installing file-0:5.47-2.fc45 100% | 5.8 MiB/s | 142.7 KiB | 00m00s [ 69/188] Installing diffutils-0:3.12-5 100% | 56.0 MiB/s | 1.6 MiB | 00m00s [ 70/188] Installing libeconf-0:0.7.9-3 100% | 80.5 MiB/s | 82.5 KiB | 00m00s [ 71/188] Installing libcap-ng-0:0.9.3- 100% | 159.0 MiB/s | 162.8 KiB | 00m00s [ 72/188] Installing audit-libs-0:4.1.4 100% | 238.9 MiB/s | 489.2 KiB | 00m00s [ 73/188] Installing pam-libs-0:1.7.2-1 100% | 219.7 MiB/s | 225.0 KiB | 00m00s [ 74/188] Installing libcap-0:2.78-1.fc 100% | 20.1 MiB/s | 513.5 KiB | 00m00s [ 75/188] Installing libsemanage-0:3.10 100% | 176.6 MiB/s | 361.7 KiB | 00m00s [ 76/188] Installing libsmartcols-0:2.4 100% | 220.2 MiB/s | 225.5 KiB | 00m00s [ 77/188] Installing alternatives-0:1.3 100% | 3.9 MiB/s | 91.6 KiB | 00m00s [ 78/188] Installing lua-libs-0:5.5.0-1 100% | 161.8 MiB/s | 331.4 KiB | 00m00s [ 79/188] Installing libffi-0:3.5.2-2.f 100% | 153.4 MiB/s | 157.1 KiB | 00m00s [ 80/188] Installing p11-kit-0:0.26.2-1 100% | 78.9 MiB/s | 2.8 MiB | 00m00s [ 81/188] Installing p11-kit-trust-0:0. 100% | 17.9 MiB/s | 531.8 KiB | 00m00s [ 82/188] Installing json-c-0:0.18-8.fc 100% | 136.5 MiB/s | 139.7 KiB | 00m00s [ 83/188] Installing ngtcp2-0:1.22.1-1. 100% | 167.3 MiB/s | 342.7 KiB | 00m00s [ 84/188] Installing openssl-libs-1:3.5 100% | 322.7 MiB/s | 7.4 MiB | 00m00s [ 85/188] Installing coreutils-0:9.11-1 100% | 168.7 MiB/s | 8.6 MiB | 00m00s [ 86/188] Installing ca-certificates-0: 100% | 1.4 MiB/s | 2.5 MiB | 00m02s [ 87/188] Installing gzip-0:1.14-2.fc44 100% | 16.6 MiB/s | 443.0 KiB | 00m00s [ 88/188] Installing rpm-sequoia-0:1.10 100% | 318.2 MiB/s | 2.2 MiB | 00m00s [ 89/188] Installing libfsverity-0:1.7- 100% | 67.6 MiB/s | 69.3 KiB | 00m00s [ 90/188] Installing libevent-0:2.1.12- 100% | 271.2 MiB/s | 1.1 MiB | 00m00s [ 91/188] Installing systemd-standalone 100% | 33.1 MiB/s | 848.5 KiB | 00m00s [ 92/188] Installing rpm-libs-0:6.0.1-5 100% | 243.3 MiB/s | 996.4 KiB | 00m00s [ 93/188] Installing ngtcp2-crypto-ossl 100% | 66.7 MiB/s | 68.3 KiB | 00m00s [ 94/188] Installing util-linux-core-0: 100% | 79.2 MiB/s | 2.5 MiB | 00m00s [ 95/188] Installing liblastlog2-0:2.42 100% | 27.3 MiB/s | 139.9 KiB | 00m00s [ 96/188] Installing zip-0:3.0-45.fc44. 100% | 28.8 MiB/s | 765.8 KiB | 00m00s [ 97/188] Installing gnupg2-keyboxd-0:2 100% | 45.8 MiB/s | 234.5 KiB | 00m00s [ 98/188] Installing libpsl-0:0.21.5-7. 100% | 130.3 MiB/s | 133.4 KiB | 00m00s [ 99/188] Installing tar-2:1.35-8.fc44. 100% | 88.4 MiB/s | 3.0 MiB | 00m00s [100/188] Installing linkdupes-0:0.7.3- 100% | 26.9 MiB/s | 715.1 KiB | 00m00s [101/188] Installing libselinux-utils-0 100% | 48.4 MiB/s | 1.4 MiB | 00m00s [102/188] Installing libfdisk-0:2.42-7. 100% | 136.7 MiB/s | 419.9 KiB | 00m00s [103/188] Installing util-linux-0:2.42- 100% | 129.8 MiB/s | 7.0 MiB | 00m00s [104/188] Installing policycoreutils-0: 100% | 38.2 MiB/s | 1.5 MiB | 00m00s [105/188] Installing selinux-policy-0:4 100% | 1.8 MiB/s | 34.6 KiB | 00m00s [106/188] Installing selinux-policy-tar 100% | 140.6 MiB/s | 14.9 MiB | 00m00s [107/188] Installing zstd-0:1.5.7-5.fc4 100% | 21.3 MiB/s | 565.8 KiB | 00m00s [108/188] Installing libxml2-0:2.12.10- 100% | 65.2 MiB/s | 1.9 MiB | 00m00s [109/188] Installing libusb1-0:1.0.29-5 100% | 22.0 MiB/s | 180.5 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.aarch64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.aarch64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [110/188] Installing tpm2-tss-0:4.1.3-9 100% | 269.6 MiB/s | 2.2 MiB | 00m00s [111/188] Installing ima-evm-utils-libs 100% | 91.7 MiB/s | 93.9 KiB | 00m00s [112/188] Installing gnupg2-gpg-agent-0 100% | 27.7 MiB/s | 850.7 KiB | 00m00s [113/188] Installing nettle-0:3.10.1-3. 100% | 187.5 MiB/s | 768.2 KiB | 00m00s [114/188] Installing gnutls-0:3.8.13-1. 100% | 309.1 MiB/s | 3.7 MiB | 00m00s [115/188] Installing bzip2-0:1.0.8-23.f 100% | 6.9 MiB/s | 175.6 KiB | 00m00s [116/188] Installing add-determinism-0: 100% | 68.0 MiB/s | 2.0 MiB | 00m00s [117/188] Installing build-reproducibil 100% | 1.5 MiB/s | 1.5 KiB | 00m00s [118/188] Installing cpio-0:2.15-9.fc44 100% | 39.1 MiB/s | 1.1 MiB | 00m00s [119/188] Installing ed-0:1.22.5-2.fc45 100% | 6.5 MiB/s | 159.9 KiB | 00m00s [120/188] Installing patch-0:2.8-4.fc44 100% | 10.7 MiB/s | 263.9 KiB | 00m00s [121/188] Installing jansson-0:2.14-4.f 100% | 92.2 MiB/s | 94.4 KiB | 00m00s [122/188] Installing lz4-libs-0:1.10.0- 100% | 193.7 MiB/s | 198.4 KiB | 00m00s [123/188] Installing libarchive-0:3.8.7 100% | 238.7 MiB/s | 977.5 KiB | 00m00s [124/188] Installing libgomp-0:16.1.1-1 100% | 290.1 MiB/s | 594.2 KiB | 00m00s [125/188] Installing libpkgconf-0:2.5.1 100% | 131.9 MiB/s | 135.1 KiB | 00m00s [126/188] Installing pkgconf-0:2.5.1-1. 100% | 4.8 MiB/s | 119.2 KiB | 00m00s [127/188] Installing pkgconf-pkg-config 100% | 77.1 KiB/s | 1.8 KiB | 00m00s [128/188] Installing libtool-ltdl-0:2.5 100% | 92.8 MiB/s | 95.0 KiB | 00m00s [129/188] Installing gdbm-libs-1:1.23-1 100% | 114.9 MiB/s | 235.4 KiB | 00m00s [130/188] Installing cyrus-sasl-lib-0:2 100% | 77.9 MiB/s | 2.4 MiB | 00m00s [131/188] Installing openldap-0:2.6.13- 100% | 187.5 MiB/s | 768.0 KiB | 00m00s [132/188] Installing gnupg2-dirmngr-0:2 100% | 21.1 MiB/s | 648.9 KiB | 00m00s [133/188] Installing gnupg2-0:2.4.9-7.f 100% | 146.8 MiB/s | 6.5 MiB | 00m00s [134/188] Installing rpm-sign-libs-0:6. 100% | 66.8 MiB/s | 68.4 KiB | 00m00s [135/188] Installing rpm-build-libs-0:6 100% | 129.3 MiB/s | 264.8 KiB | 00m00s [136/188] Installing gpgverify-0:2.2-4. 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [137/188] Installing xxhash-libs-0:0.8. 100% | 85.1 MiB/s | 87.2 KiB | 00m00s [138/188] Installing libbrotli-0:1.2.0- 100% | 222.5 MiB/s | 911.3 KiB | 00m00s [139/188] Installing libnghttp2-0:1.69. 100% | 194.4 MiB/s | 199.0 KiB | 00m00s [140/188] Installing libnghttp3-0:1.15. 100% | 203.1 MiB/s | 208.0 KiB | 00m00s [141/188] Installing keyutils-libs-0:1. 100% | 97.3 MiB/s | 99.6 KiB | 00m00s [142/188] Installing libcom_err-0:1.47. 100% | 109.6 MiB/s | 112.2 KiB | 00m00s [143/188] Installing libverto-0:0.3.2-1 100% | 69.4 MiB/s | 71.1 KiB | 00m00s [144/188] Installing krb5-libs-0:1.22.2 100% | 253.4 MiB/s | 2.5 MiB | 00m00s [145/188] Installing libcbor-0:0.14.0-2 100% | 137.7 MiB/s | 141.0 KiB | 00m00s [146/188] Installing libfido2-0:1.17.0- 100% | 275.6 MiB/s | 282.2 KiB | 00m00s [147/188] Installing libssh-0:0.12.0-1. 100% | 234.7 MiB/s | 721.0 KiB | 00m00s [148/188] Installing libcurl-0:8.20.0~r 100% | 239.9 MiB/s | 982.8 KiB | 00m00s [149/188] Installing elfutils-debuginfo 100% | 5.7 MiB/s | 146.2 KiB | 00m00s [150/188] Installing binutils-0:2.46.50 100% | 291.6 MiB/s | 31.5 MiB | 00m00s [151/188] Installing elfutils-0:0.195-1 100% | 108.7 MiB/s | 3.6 MiB | 00m00s [152/188] Installing gdb-minimal-0:17.1 100% | 218.3 MiB/s | 13.5 MiB | 00m00s [153/188] Installing debugedit-0:5.3-2. 100% | 12.7 MiB/s | 324.2 KiB | 00m00s [154/188] Installing curl-0:8.20.0~rc3- 100% | 14.2 MiB/s | 465.7 KiB | 00m00s [155/188] Installing rpm-0:6.0.1-5.fc45 100% | 59.4 MiB/s | 2.8 MiB | 00m00s [156/188] Installing cmake-srpm-macros- 100% | 785.2 KiB/s | 804.0 B | 00m00s [157/188] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [158/188] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [159/188] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [160/188] Installing tree-sitter-srpm-m 100% | 9.1 MiB/s | 9.3 KiB | 00m00s [161/188] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [162/188] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [163/188] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [164/188] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [165/188] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [166/188] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [167/188] Installing package-notes-srpm 100% | 0.0 B/s | 2.1 KiB | 00m00s [168/188] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [169/188] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [170/188] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [171/188] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [172/188] Installing ghc-srpm-macros-0: 100% | 173.8 KiB/s | 1.0 KiB | 00m00s [173/188] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [174/188] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [175/188] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [176/188] Installing redhat-rpm-config- 100% | 92.7 MiB/s | 189.9 KiB | 00m00s [177/188] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [178/188] Installing rpm-build-0:6.0.1- 100% | 22.0 MiB/s | 606.9 KiB | 00m00s [179/188] Installing erlang-srpm-macros 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [180/188] Installing pyproject-srpm-mac 100% | 0.0 B/s | 3.8 KiB | 00m00s [181/188] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [182/188] Installing go-srpm-macros-0:3 100% | 61.6 MiB/s | 63.0 KiB | 00m00s [183/188] Installing R-srpm-macros-0:1. 100% | 4.3 MiB/s | 4.4 KiB | 00m00s [184/188] Installing python-srpm-macros 100% | 51.7 MiB/s | 52.9 KiB | 00m00s [185/188] Installing rpm-plugin-selinux 100% | 67.2 MiB/s | 68.8 KiB | 00m00s [186/188] Installing which-0:2.23-4.fc4 100% | 4.9 MiB/s | 125.5 KiB | 00m00s [187/188] Installing shadow-utils-2:4.1 100% | 93.6 MiB/s | 4.5 MiB | 00m00s [188/188] Installing info-0:7.3-1.fc45. 100% | 50.9 KiB/s | 424.7 KiB | 00m08s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.7-2.fc45.noarch add-determinism-0.7.3-2.fc45.aarch64 alternatives-1.33-5.fc44.aarch64 ansible-srpm-macros-1-20.1.fc44.noarch audit-libs-4.1.4-1.fc45.aarch64 bash-5.3.9-3.fc44.aarch64 binutils-2.46.50-7.fc45.aarch64 build-reproducibility-srpm-macros-0.7.3-2.fc45.noarch bzip2-1.0.8-23.fc44.aarch64 bzip2-libs-1.0.8-23.fc44.aarch64 ca-certificates-2025.2.80_v9.0.304-7.fc45.noarch cmake-srpm-macros-4.3.0-1.fc45.noarch coreutils-9.11-1.fc45.aarch64 coreutils-common-9.11-1.fc45.aarch64 cpio-2.15-9.fc44.aarch64 crypto-policies-20251128-3.git19878fe.fc44.noarch curl-8.20.0~rc3-1.fc45.aarch64 cyrus-sasl-lib-2.1.28-35.fc44.aarch64 debugedit-5.3-2.fc45.aarch64 diffutils-3.12-5.fc44.aarch64 dwz-0.16-3.fc44.aarch64 ed-1.22.5-2.fc45.aarch64 efi-srpm-macros-6-6.fc44.noarch elfutils-0.195-1.fc45.aarch64 elfutils-debuginfod-client-0.195-1.fc45.aarch64 elfutils-libelf-0.195-1.fc45.aarch64 elfutils-libs-0.195-1.fc45.aarch64 erlang-srpm-macros-0.3.11-1.fc45.noarch fedora-gpg-keys-45-0.1.noarch fedora-release-45-0.7.noarch fedora-release-common-45-0.7.noarch fedora-release-identity-basic-45-0.7.noarch fedora-repos-45-0.1.noarch fedora-repos-rawhide-45-0.1.noarch file-5.47-2.fc45.aarch64 file-libs-5.47-2.fc45.aarch64 filesystem-3.18-56.fc45.aarch64 filesystem-srpm-macros-3.18-56.fc45.noarch findutils-4.10.0-7.fc44.aarch64 fonts-srpm-macros-5.0.0-3.fc45.noarch forge-srpm-macros-0.4.0-4.fc44.noarch fpc-srpm-macros-1.3-16.fc44.noarch gap-srpm-macros-2-2.fc44.noarch gawk-5.4.0-2.fc45.aarch64 gdb-minimal-17.1-5.fc45.aarch64 gdbm-libs-1.23-11.fc44.aarch64 ghc-srpm-macros-1.10-1.fc44.noarch glibc-2.43.9000-14.fc45.aarch64 glibc-common-2.43.9000-14.fc45.aarch64 glibc-gconv-extra-2.43.9000-14.fc45.aarch64 glibc-minimal-langpack-2.43.9000-14.fc45.aarch64 gmp-6.3.0-5.fc44.aarch64 gnat-srpm-macros-7-2.fc44.noarch gnulib-l10n-20241231-2.fc44.noarch gnupg2-2.4.9-7.fc45.aarch64 gnupg2-dirmngr-2.4.9-7.fc45.aarch64 gnupg2-gpg-agent-2.4.9-7.fc45.aarch64 gnupg2-gpgconf-2.4.9-7.fc45.aarch64 gnupg2-keyboxd-2.4.9-7.fc45.aarch64 gnupg2-verify-2.4.9-7.fc45.aarch64 gnutls-3.8.13-1.fc45.aarch64 go-srpm-macros-3.8.0-2.fc44.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-d924b10d3e810dabdd8b56b596e7e91491211fce-697c9899 gpgverify-2.2-4.fc44.noarch grep-3.12-3.fc44.aarch64 gzip-1.14-2.fc44.aarch64 ima-evm-utils-libs-1.6.2-10.fc45.aarch64 info-7.3-1.fc45.aarch64 jansson-2.14-4.fc44.aarch64 java-srpm-macros-1-8.fc44.noarch json-c-0.18-8.fc44.aarch64 kernel-srpm-macros-1.0-29.fc45.noarch keyutils-libs-1.6.3-7.fc44.aarch64 krb5-libs-1.22.2-7.fc45.aarch64 libacl-2.3.2-6.fc44.aarch64 libarchive-3.8.7-1.fc45.aarch64 libassuan-2.5.7-5.fc44.aarch64 libattr-2.5.2-8.fc44.aarch64 libblkid-2.42-7.fc45.aarch64 libbrotli-1.2.0-3.fc44.aarch64 libcap-2.78-1.fc45.aarch64 libcap-ng-0.9.3-1.fc45.aarch64 libcbor-0.14.0-2.fc45.aarch64 libcom_err-1.47.4-1.fc45.aarch64 libcurl-8.20.0~rc3-1.fc45.aarch64 libeconf-0.7.9-3.fc44.aarch64 libevent-2.1.12-17.fc44.aarch64 libfdisk-2.42-7.fc45.aarch64 libffi-3.5.2-2.fc44.aarch64 libfido2-1.17.0-2.fc45.aarch64 libfsverity-1.7-1.fc45.aarch64 libgcc-16.1.1-1.fc45.aarch64 libgcrypt-1.12.2-1.fc45.aarch64 libgomp-16.1.1-1.fc45.aarch64 libgpg-error-1.60-1.fc45.aarch64 libidn2-2.3.8-3.fc44.aarch64 libksba-1.6.8-1.fc45.aarch64 liblastlog2-2.42-7.fc45.aarch64 libmount-2.42-7.fc45.aarch64 libnghttp2-1.69.0-1.fc45.aarch64 libnghttp3-1.15.0-1.fc44.aarch64 libpkgconf-2.5.1-1.fc45.aarch64 libpsl-0.21.5-7.fc44.aarch64 libselinux-3.10-1.fc44.aarch64 libselinux-utils-3.10-1.fc44.aarch64 libsemanage-3.10-1.fc44.aarch64 libsepol-3.10-1.fc44.aarch64 libsmartcols-2.42-7.fc45.aarch64 libssh-0.12.0-1.fc45.aarch64 libssh-config-0.12.0-1.fc45.noarch libstdc++-16.1.1-1.fc45.aarch64 libtasn1-4.21.0-1.fc45.aarch64 libtool-ltdl-2.5.4-10.fc44.aarch64 libunistring-1.1-11.fc44.aarch64 libusb1-1.0.29-5.fc44.aarch64 libuuid-2.42-7.fc45.aarch64 libverto-0.3.2-12.fc44.aarch64 libxcrypt-4.5.2-3.fc44.aarch64 libxml2-2.12.10-6.fc44.aarch64 libzstd-1.5.7-5.fc44.aarch64 linkdupes-0.7.3-2.fc45.aarch64 lua-libs-5.5.0-1.fc45.aarch64 lua-srpm-macros-1-17.fc44.noarch lz4-libs-1.10.0-4.fc44.aarch64 mpfr-4.2.2-3.fc44.aarch64 ncurses-base-6.6-2.fc45.noarch ncurses-libs-6.6-2.fc45.aarch64 nettle-3.10.1-3.fc44.aarch64 ngtcp2-1.22.1-1.fc45.aarch64 ngtcp2-crypto-ossl-1.22.1-1.fc45.aarch64 npth-1.8-4.fc44.aarch64 ocaml-srpm-macros-11-3.fc44.noarch openblas-srpm-macros-2-21.fc44.noarch openldap-2.6.13-1.fc45.aarch64 openssl-libs-3.5.6-1.fc45.aarch64 p11-kit-0.26.2-1.fc45.aarch64 p11-kit-trust-0.26.2-1.fc45.aarch64 package-notes-srpm-macros-0.17-3.fc45.noarch pam-libs-1.7.2-1.fc44.aarch64 patch-2.8-4.fc44.aarch64 pcre2-10.47-1.fc44.1.aarch64 pcre2-syntax-10.47-1.fc44.1.noarch perl-srpm-macros-1-61.fc44.noarch pkgconf-2.5.1-1.fc45.aarch64 pkgconf-m4-2.5.1-1.fc45.noarch pkgconf-pkg-config-2.5.1-1.fc45.aarch64 policycoreutils-3.10-3.fc45.aarch64 popt-1.19-10.fc44.aarch64 publicsuffix-list-dafsa-20260116-1.fc44.noarch pyproject-srpm-macros-1.22.0-1.fc45.noarch python-srpm-macros-3.14-12.fc45.noarch qt5-srpm-macros-5.15.18-2.fc44.noarch qt6-srpm-macros-6.11.0-1.fc45.noarch readline-8.3-4.fc44.aarch64 redhat-rpm-config-344-1.fc45.noarch redhat-systemd-presets-102-1.fc45.noarch redhat-systemd-presets-common-102-1.fc45.noarch rpm-6.0.1-5.fc45.aarch64 rpm-build-6.0.1-5.fc45.aarch64 rpm-build-libs-6.0.1-5.fc45.aarch64 rpm-libs-6.0.1-5.fc45.aarch64 rpm-plugin-selinux-6.0.1-5.fc45.aarch64 rpm-sequoia-1.10.2-1.fc45.aarch64 rpm-sign-libs-6.0.1-5.fc45.aarch64 rust-srpm-macros-28.4-3.fc44.noarch sed-4.10-1.fc45.aarch64 selinux-policy-45.2-1.fc45.noarch selinux-policy-targeted-45.2-1.fc45.noarch setup-2.15.0-29.fc45.noarch shadow-utils-4.19.3-2.fc45.aarch64 sqlite-libs-3.53.0-1.fc45.aarch64 systemd-libs-260.1-2.fc45.aarch64 systemd-standalone-sysusers-260.1-2.fc45.aarch64 tar-1.35-8.fc44.aarch64 tpm2-tss-4.1.3-9.fc44.aarch64 tree-sitter-srpm-macros-0.4.3-1.fc45.noarch unzip-6.0-69.fc44.aarch64 util-linux-2.42-7.fc45.aarch64 util-linux-core-2.42-7.fc45.aarch64 which-2.23-4.fc44.aarch64 xxhash-libs-0.8.3-4.fc44.aarch64 xz-5.8.3-1.fc45.aarch64 xz-libs-5.8.3-1.fc45.aarch64 zig-srpm-macros-1-8.fc44.noarch zip-3.0-45.fc44.aarch64 zlib-ng-compat-2.3.3-5.fc45.aarch64 zstd-1.5.7-5.fc44.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1778317779.858557/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-blo3kfh8/python-pysam/python-pysam.spec) Config(child) 0 minutes 26 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-0.24.0-1.fc45.src.rpm) Config(fedora-rawhide-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1778317779.858557/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1778317779.858557/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-aarch64-1778317779.858557/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-5.fc45.aarch64 rpm-sequoia-1.10.2-1.fc45.aarch64 dnf5-5.4.2.0-1.fc45.aarch64 dnf5-plugins-5.4.2.0-1.fc45.aarch64 Finish: chroot init Start: build phase for python-pysam-0.24.0-1.fc45.src.rpm Start: build setup for python-pysam-0.24.0-1.fc45.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.src.rpm Updating and loading repositories: fedora 100% | 96.8 KiB/s | 14.8 KiB | 00m00s Copr repository 100% | 138.0 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel aarch64 0:1.0.8-23.fc44 fedora 309.8 KiB gcc aarch64 0:16.1.1-1.fc45 fedora 112.4 MiB python3-cython aarch64 0:3.2.4-3.fc44 fedora 19.0 MiB python3-devel aarch64 0:3.14.4-2.fc45 fedora 2.0 MiB python3-sphinx noarch 1:9.1.0-1.fc45 fedora 13.8 MiB python3-sphinx_rtd_theme noarch 0:3.1.0-2.fc44 fedora 327.5 KiB xz-devel aarch64 1:5.8.3-1.fc45 fedora 258.8 KiB zlib-ng-compat-devel aarch64 0:2.3.3-5.fc45 fedora 107.0 KiB Installing dependencies: annobin-docs noarch 0:13.14-1.fc45 fedora 99.3 KiB annobin-plugin-gcc aarch64 0:13.14-1.fc45 fedora 711.3 KiB cmake-filesystem aarch64 0:4.3.0-1.fc45 fedora 0.0 B cpp aarch64 0:16.1.1-1.fc45 fedora 40.8 MiB expat aarch64 0:2.7.5-1.fc45 fedora 367.0 KiB fontawesome4-fonts noarch 1:4.7.0-26.fc44 fedora 296.6 KiB fonts-filesystem noarch 1:5.0.0-3.fc45 fedora 0.0 B gcc-plugin-annobin aarch64 0:16.1.1-1.fc45 fedora 69.2 KiB glibc-devel aarch64 0:2.43.9000-14.fc45 fedora 2.3 MiB google-roboto-slab-fonts noarch 0:1.100263-0.28.20150923git.fc44 fedora 699.6 KiB kernel-headers aarch64 0:7.1.0-0.rc1.9.fc45 fedora 6.8 MiB lato-fonts noarch 0:2.015-25.fc44 fedora 11.3 MiB libasan aarch64 0:16.1.1-1.fc45 fedora 1.5 MiB libatomic aarch64 0:16.1.1-1.fc45 fedora 77.7 KiB libmpc aarch64 0:1.4.1-1.fc45 fedora 216.8 KiB libubsan aarch64 0:16.1.1-1.fc45 fedora 475.9 KiB libxcrypt-devel aarch64 0:4.5.2-3.fc44 fedora 31.0 KiB make aarch64 1:4.4.1-12.fc44 fedora 1.8 MiB mpdecimal aarch64 0:4.0.1-3.fc44 fedora 281.1 KiB pyproject-rpm-macros noarch 0:1.22.0-1.fc45 fedora 146.4 KiB python-pip-wheel noarch 0:26.0.1-2.fc45 fedora 1.2 MiB python-rpm-macros noarch 0:3.14-12.fc45 fedora 28.0 KiB python3 aarch64 0:3.14.4-2.fc45 fedora 84.8 KiB python3-babel noarch 0:2.18.0-1.fc45 fedora 30.3 MiB python3-charset-normalizer noarch 0:3.4.7-1.fc45 fedora 405.6 KiB python3-docutils noarch 0:0.22.4-2.fc44 fedora 5.5 MiB python3-idna noarch 0:3.13-1.fc45 fedora 597.5 KiB python3-imagesize noarch 0:2.0.0-1.fc45 fedora 82.4 KiB python3-jinja2 noarch 0:3.1.6-7.fc44 fedora 3.1 MiB python3-libs aarch64 0:3.14.4-2.fc45 fedora 45.4 MiB python3-markupsafe aarch64 0:3.0.2-7.fc44 fedora 117.4 KiB python3-packaging noarch 0:26.2-1.fc45 fedora 1.0 MiB python3-pygments noarch 0:2.19.2-1.fc45 fedora 11.3 MiB python3-requests noarch 0:2.33.1-1.fc45 fedora 477.3 KiB python3-roman-numerals noarch 0:4.1.0-1.fc45 fedora 40.8 KiB python3-rpm-generators noarch 0:14-15.fc45 fedora 81.7 KiB python3-rpm-macros noarch 0:3.14-12.fc45 fedora 6.5 KiB python3-snowballstemmer noarch 0:3.0.1-11.fc44 fedora 1.8 MiB python3-sphinx-theme-alabaster noarch 0:0.7.16-12.fc44 fedora 42.0 KiB python3-sphinxcontrib-jquery noarch 0:4.1-15.fc44 fedora 382.5 KiB python3-urllib3 noarch 0:2.6.3-3.fc45 fedora 1.1 MiB tzdata noarch 0:2026a-1.fc45 fedora 1.2 MiB Transaction Summary: Installing: 50 packages Total size of inbound packages is 94 MiB. Need to download 94 MiB. After this operation, 320 MiB extra will be used (install 320 MiB, remove 0 B). [ 1/50] bzip2-devel-0:1.0.8-23.fc44.aar 100% | 34.8 MiB/s | 213.6 KiB | 00m00s [ 2/50] python3-devel-0:3.14.4-2.fc45.a 100% | 47.5 MiB/s | 437.7 KiB | 00m00s [ 3/50] python3-sphinx_rtd_theme-0:3.1. 100% | 28.2 MiB/s | 86.6 KiB | 00m00s [ 4/50] python3-sphinx-1:9.1.0-1.fc45.n 100% | 196.2 MiB/s | 3.1 MiB | 00m00s [ 5/50] xz-devel-1:5.8.3-1.fc45.aarch64 100% | 21.6 MiB/s | 66.4 KiB | 00m00s [ 6/50] zlib-ng-compat-devel-0:2.3.3-5. 100% | 12.4 MiB/s | 38.2 KiB | 00m00s [ 7/50] cpp-0:16.1.1-1.fc45.aarch64 100% | 221.6 MiB/s | 13.3 MiB | 00m00s [ 8/50] glibc-devel-0:2.43.9000-14.fc45 100% | 47.1 MiB/s | 626.4 KiB | 00m00s [ 9/50] libasan-0:16.1.1-1.fc45.aarch64 100% | 99.6 MiB/s | 509.9 KiB | 00m00s [10/50] libatomic-0:16.1.1-1.fc45.aarch 100% | 24.1 MiB/s | 49.3 KiB | 00m00s [11/50] libmpc-0:1.4.1-1.fc45.aarch64 100% | 36.0 MiB/s | 73.7 KiB | 00m00s [12/50] libubsan-0:16.1.1-1.fc45.aarch6 100% | 43.3 MiB/s | 221.9 KiB | 00m00s [13/50] make-1:4.4.1-12.fc44.aarch64 100% | 95.0 MiB/s | 583.6 KiB | 00m00s [14/50] python3-0:3.14.4-2.fc45.aarch64 100% | 9.4 MiB/s | 28.9 KiB | 00m00s [15/50] python3-libs-0:3.14.4-2.fc45.aa 100% | 209.9 MiB/s | 9.9 MiB | 00m00s [16/50] fontawesome4-fonts-1:4.7.0-26.f 100% | 49.9 MiB/s | 204.2 KiB | 00m00s [17/50] google-roboto-slab-fonts-0:1.10 100% | 58.4 MiB/s | 239.1 KiB | 00m00s [18/50] gcc-0:16.1.1-1.fc45.aarch64 100% | 167.3 MiB/s | 39.8 MiB | 00m00s [19/50] lato-fonts-0:2.015-25.fc44.noar 100% | 59.5 MiB/s | 3.1 MiB | 00m00s [20/50] python3-docutils-0:0.22.4-2.fc4 100% | 83.8 MiB/s | 1.2 MiB | 00m00s [21/50] python3-sphinxcontrib-jquery-0: 100% | 27.9 MiB/s | 114.3 KiB | 00m00s [22/50] python3-imagesize-0:2.0.0-1.fc4 100% | 11.6 MiB/s | 35.6 KiB | 00m00s [23/50] python3-jinja2-0:3.1.6-7.fc44.n 100% | 71.9 MiB/s | 515.5 KiB | 00m00s [24/50] python3-packaging-0:26.2-1.fc45 100% | 25.7 MiB/s | 237.0 KiB | 00m00s [25/50] python3-babel-0:2.18.0-1.fc45.n 100% | 216.8 MiB/s | 6.9 MiB | 00m00s [26/50] python3-pygments-0:2.19.2-1.fc4 100% | 41.8 MiB/s | 2.7 MiB | 00m00s [27/50] python3-requests-0:2.33.1-1.fc4 100% | 2.7 MiB/s | 160.6 KiB | 00m00s [28/50] python3-snowballstemmer-0:3.0.1 100% | 91.4 MiB/s | 280.6 KiB | 00m00s [29/50] python3-roman-numerals-0:4.1.0- 100% | 2.2 MiB/s | 19.8 KiB | 00m00s [30/50] python3-sphinx-theme-alabaster- 100% | 7.9 MiB/s | 24.4 KiB | 00m00s [31/50] cmake-filesystem-0:4.3.0-1.fc45 100% | 2.9 MiB/s | 15.0 KiB | 00m00s [32/50] libxcrypt-devel-0:4.5.2-3.fc44. 100% | 5.9 MiB/s | 30.0 KiB | 00m00s [33/50] kernel-headers-0:7.1.0-0.rc1.9. 100% | 171.0 MiB/s | 1.7 MiB | 00m00s [34/50] expat-0:2.7.5-1.fc45.aarch64 100% | 39.7 MiB/s | 122.1 KiB | 00m00s [35/50] mpdecimal-0:4.0.1-3.fc44.aarch6 100% | 46.6 MiB/s | 95.4 KiB | 00m00s [36/50] python-pip-wheel-0:26.0.1-2.fc4 100% | 164.2 MiB/s | 1.1 MiB | 00m00s [37/50] tzdata-0:2026a-1.fc45.noarch 100% | 87.1 MiB/s | 713.3 KiB | 00m00s [38/50] fonts-filesystem-1:5.0.0-3.fc45 100% | 2.8 MiB/s | 8.7 KiB | 00m00s [39/50] python3-markupsafe-0:3.0.2-7.fc 100% | 15.4 MiB/s | 31.6 KiB | 00m00s [40/50] python3-charset-normalizer-0:3. 100% | 63.0 MiB/s | 129.1 KiB | 00m00s [41/50] python3-idna-0:3.13-1.fc45.noar 100% | 5.1 MiB/s | 116.0 KiB | 00m00s [42/50] annobin-plugin-gcc-0:13.14-1.fc 100% | 133.6 MiB/s | 684.2 KiB | 00m00s [43/50] gcc-plugin-annobin-0:16.1.1-1.f 100% | 25.6 MiB/s | 52.4 KiB | 00m00s [44/50] annobin-docs-0:13.14-1.fc45.noa 100% | 42.4 MiB/s | 86.9 KiB | 00m00s [45/50] pyproject-rpm-macros-0:1.22.0-1 100% | 17.1 MiB/s | 52.5 KiB | 00m00s [46/50] python-rpm-macros-0:3.14-12.fc4 100% | 6.5 MiB/s | 20.0 KiB | 00m00s [47/50] python3-rpm-generators-0:14-15. 100% | 9.3 MiB/s | 28.5 KiB | 00m00s [48/50] python3-rpm-macros-0:3.14-12.fc 100% | 4.1 MiB/s | 12.5 KiB | 00m00s [49/50] python3-urllib3-0:2.6.3-3.fc45. 100% | 5.7 MiB/s | 301.7 KiB | 00m00s [50/50] python3-cython-0:3.2.4-3.fc44.a 100% | 5.8 MiB/s | 4.0 MiB | 00m01s -------------------------------------------------------------------------------- [50/50] Total 100% | 132.1 MiB/s | 93.9 MiB | 00m01s Running transaction [ 1/52] Verify package files 100% | 167.0 B/s | 50.0 B | 00m00s [ 2/52] Prepare transaction 100% | 543.0 B/s | 50.0 B | 00m00s [ 3/52] Installing python-rpm-macros-0: 100% | 28.2 MiB/s | 28.9 KiB | 00m00s [ 4/52] Installing fonts-filesystem-1:5 100% | 0.0 B/s | 788.0 B | 00m00s [ 5/52] Installing python3-rpm-macros-0 100% | 0.0 B/s | 6.8 KiB | 00m00s [ 6/52] Installing libmpc-0:1.4.1-1.fc4 100% | 106.7 MiB/s | 218.5 KiB | 00m00s [ 7/52] Installing cpp-0:16.1.1-1.fc45. 100% | 279.2 MiB/s | 40.8 MiB | 00m00s [ 8/52] Installing pyproject-rpm-macros 100% | 145.2 MiB/s | 148.7 KiB | 00m00s [ 9/52] Installing fontawesome4-fonts-1 100% | 145.4 MiB/s | 297.8 KiB | 00m00s [10/52] Installing google-roboto-slab-f 100% | 228.3 MiB/s | 701.4 KiB | 00m00s [11/52] Installing lato-fonts-0:2.015-2 100% | 343.5 MiB/s | 11.3 MiB | 00m00s [12/52] Installing annobin-docs-0:13.14 100% | 19.6 MiB/s | 100.5 KiB | 00m00s [13/52] Installing tzdata-0:2026a-1.fc4 100% | 29.1 MiB/s | 1.5 MiB | 00m00s [14/52] Installing python-pip-wheel-0:2 100% | 407.6 MiB/s | 1.2 MiB | 00m00s [15/52] Installing mpdecimal-0:4.0.1-3. 100% | 138.0 MiB/s | 282.6 KiB | 00m00s [16/52] Installing expat-0:2.7.5-1.fc45 100% | 12.0 MiB/s | 369.1 KiB | 00m00s [17/52] Installing python3-libs-0:3.14. 100% | 266.3 MiB/s | 45.8 MiB | 00m00s [18/52] Installing python3-0:3.14.4-2.f 100% | 3.3 MiB/s | 86.5 KiB | 00m00s [19/52] Installing python3-docutils-0:0 100% | 107.4 MiB/s | 5.6 MiB | 00m00s [20/52] Installing python3-packaging-0: 100% | 198.9 MiB/s | 1.0 MiB | 00m00s [21/52] Installing python3-idna-0:3.13- 100% | 196.6 MiB/s | 604.0 KiB | 00m00s [22/52] Installing python3-urllib3-0:2. 100% | 162.5 MiB/s | 1.1 MiB | 00m00s [23/52] Installing python3-rpm-generato 100% | 20.2 MiB/s | 82.9 KiB | 00m00s [24/52] Installing python3-babel-0:2.18 100% | 265.3 MiB/s | 30.5 MiB | 00m00s [25/52] Installing python3-imagesize-0: 100% | 16.7 MiB/s | 85.5 KiB | 00m00s [26/52] Installing python3-pygments-0:2 100% | 147.8 MiB/s | 11.5 MiB | 00m00s [27/52] Installing python3-roman-numera 100% | 21.3 MiB/s | 43.7 KiB | 00m00s [28/52] Installing python3-snowballstem 100% | 232.5 MiB/s | 1.9 MiB | 00m00s [29/52] Installing python3-sphinx-theme 100% | 22.8 MiB/s | 46.6 KiB | 00m00s [30/52] Installing python3-markupsafe-0 100% | 59.4 MiB/s | 121.7 KiB | 00m00s [31/52] Installing python3-jinja2-0:3.1 100% | 281.1 MiB/s | 3.1 MiB | 00m00s [32/52] Installing python3-charset-norm 100% | 15.0 MiB/s | 415.8 KiB | 00m00s [33/52] Installing python3-requests-0:2 100% | 68.3 MiB/s | 489.5 KiB | 00m00s [34/52] Installing python3-sphinx-1:9.1 100% | 137.5 MiB/s | 14.0 MiB | 00m00s [35/52] Installing python3-sphinxcontri 100% | 75.4 MiB/s | 386.1 KiB | 00m00s [36/52] Installing kernel-headers-0:7.1 100% | 142.4 MiB/s | 7.0 MiB | 00m00s [37/52] Installing glibc-devel-0:2.43.9 100% | 112.4 MiB/s | 2.4 MiB | 00m00s [38/52] Installing libxcrypt-devel-0:4. 100% | 32.5 MiB/s | 33.3 KiB | 00m00s [39/52] Installing cmake-filesystem-0:4 100% | 3.0 MiB/s | 9.4 KiB | 00m00s [40/52] Installing make-1:4.4.1-12.fc44 100% | 59.7 MiB/s | 1.9 MiB | 00m00s [41/52] Installing libubsan-0:16.1.1-1. 100% | 232.8 MiB/s | 476.8 KiB | 00m00s [42/52] Installing libatomic-0:16.1.1-1 100% | 77.0 MiB/s | 78.8 KiB | 00m00s [43/52] Installing libasan-0:16.1.1-1.f 100% | 256.9 MiB/s | 1.5 MiB | 00m00s [44/52] Installing gcc-0:16.1.1-1.fc45. 100% | 334.7 MiB/s | 112.5 MiB | 00m00s [45/52] Installing annobin-plugin-gcc-0 100% | 53.6 MiB/s | 713.0 KiB | 00m00s [46/52] Installing gcc-plugin-annobin-0 100% | 4.9 MiB/s | 70.8 KiB | 00m00s [47/52] Installing zlib-ng-compat-devel 100% | 106.0 MiB/s | 108.6 KiB | 00m00s [48/52] Installing python3-sphinx_rtd_t 100% | 42.5 MiB/s | 348.4 KiB | 00m00s [49/52] Installing python3-devel-0:3.14 100% | 51.4 MiB/s | 2.0 MiB | 00m00s [50/52] Installing python3-cython-0:3.2 100% | 207.9 MiB/s | 19.1 MiB | 00m00s [51/52] Installing xz-devel-1:5.8.3-1.f 100% | 128.2 MiB/s | 262.6 KiB | 00m00s [52/52] Installing bzip2-devel-0:1.0.8- 100% | 2.2 MiB/s | 310.7 KiB | 00m00s Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.src.rpm Updating and loading repositories: fedora 100% | 83.7 KiB/s | 14.8 KiB | 00m00s Copr repository 100% | 43.4 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-23.fc44.aarch64" is already installed. Package "gcc-16.1.1-1.fc45.aarch64" is already installed. Package "python3-devel-3.14.4-2.fc45.aarch64" is already installed. Package "python3-sphinx_rtd_theme-3.1.0-2.fc44.noarch" is already installed. Package "python3-cython-3.2.4-3.fc44.aarch64" is already installed. Package "python3-sphinx-1:9.1.0-1.fc45.noarch" is already installed. Package "xz-devel-1:5.8.3-1.fc45.aarch64" is already installed. Package "zlib-ng-compat-devel-2.3.3-5.fc45.aarch64" is already installed. Nothing to do. Finish: build setup for python-pysam-0.24.0-1.fc45.src.rpm Start: rpmbuild python-pysam-0.24.0-1.fc45.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.9I9C4O Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.WYi6pR + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd /builddir/build/BUILD/python-pysam-0.24.0-build + rm -rf pysam-0.24.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.24.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.24.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . ++ 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(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.AouCfq + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir --output /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires --dep-overrides-file /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-dep-overrides Handling setuptools>=59.0 from build-system.requires Requirement not satisfied: setuptools>=59.0 Handling Cython>=3,<4 from build-system.requires Requirement satisfied: Cython>=3,<4 (installed: Cython 3.2.4) Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 90.3 KiB/s | 14.8 KiB | 00m00s Copr repository 100% | 72.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-23.fc44.aarch64" is already installed. Package "gcc-16.1.1-1.fc45.aarch64" is already installed. Package "pyproject-rpm-macros-1.22.0-1.fc45.noarch" is already installed. Package "python3-devel-3.14.4-2.fc45.aarch64" is already installed. Package "python3-sphinx_rtd_theme-3.1.0-2.fc44.noarch" is already installed. Package Arch Version Repository Size Installing: python3-pip noarch 0:26.0.1-2.fc45 fedora 11.4 MiB python3-setuptools noarch 0:80.10.2-3.fc45 fedora 7.5 MiB Transaction Summary: Installing: 2 packages Package "python3-cython-3.2.4-3.fc44.aarch64" is already installed. Package "python3-packaging-26.2-1.fc45.noarch" is already installed. Package "python3-sphinx-1:9.1.0-1.fc45.noarch" is already installed. Package "xz-devel-1:5.8.3-1.fc45.aarch64" is already installed. Package "zlib-ng-compat-devel-2.3.3-5.fc45.aarch64" is already installed. Total size of inbound packages is 4 MiB. Need to download 4 MiB. After this operation, 19 MiB extra will be used (install 19 MiB, remove 0 B). [1/2] python3-pip-0:26.0.1-2.fc45.noarc 100% | 177.7 MiB/s | 2.7 MiB | 00m00s [2/2] python3-setuptools-0:80.10.2-3.fc 100% | 29.2 MiB/s | 1.8 MiB | 00m00s -------------------------------------------------------------------------------- [2/2] Total 100% | 60.5 MiB/s | 4.4 MiB | 00m00s Running transaction [1/4] Verify package files 100% | 142.0 B/s | 2.0 B | 00m00s [2/4] Prepare transaction 100% | 54.0 B/s | 2.0 B | 00m00s [3/4] Installing python3-setuptools-0:8 100% | 136.6 MiB/s | 7.7 MiB | 00m00s [4/4] Installing python3-pip-0:26.0.1-2 100% | 93.1 MiB/s | 11.7 MiB | 00m00s Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.ntz9IK + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir --output /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires --dep-overrides-file /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-dep-overrides Handling setuptools>=59.0 from build-system.requires Requirement satisfied: setuptools>=59.0 (installed: setuptools 80.10.2) Handling Cython>=3,<4 from build-system.requires Requirement satisfied: Cython>=3,<4 (installed: Cython 3.2.4) # pysam: Cython 3.2.4 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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 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' 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' # pysam: Cython 3.2.4 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 -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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 dist_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' 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' creating '/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam-0.24.0.dist-info' + cat /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires + rm -rfv pysam-0.24.0.dist-info/ removed 'pysam-0.24.0.dist-info/licenses/AUTHORS' removed 'pysam-0.24.0.dist-info/licenses/COPYING' removed directory 'pysam-0.24.0.dist-info/licenses' removed 'pysam-0.24.0.dist-info/METADATA' removed 'pysam-0.24.0.dist-info/top_level.txt' removed directory 'pysam-0.24.0.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 92.0 KiB/s | 14.8 KiB | 00m00s Copr repository 100% | 75.9 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-23.fc44.aarch64" is already installed. Package "gcc-16.1.1-1.fc45.aarch64" is already installed. Package "pyproject-rpm-macros-1.22.0-1.fc45.noarch" is already installed. Package "python3-devel-3.14.4-2.fc45.aarch64" is already installed. Package "python3-sphinx_rtd_theme-3.1.0-2.fc44.noarch" is already installed. Package "python3-cython-3.2.4-3.fc44.aarch64" is already installed. Package "python3-packaging-26.2-1.fc45.noarch" is already installed. Package "python3-pip-26.0.1-2.fc45.noarch" is already installed. Package "python3-setuptools-80.10.2-3.fc45.noarch" is already installed. Package "python3-sphinx-1:9.1.0-1.fc45.noarch" is already installed. Package "xz-devel-1:5.8.3-1.fc45.aarch64" is already installed. Package "zlib-ng-compat-devel-2.3.3-5.fc45.aarch64" is already installed. Nothing to do. Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1778284800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.le0E8e + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + RPM_TOXENV=py314 + FEDORA=45 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir --output /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires --dep-overrides-file /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-dep-overrides Handling setuptools>=59.0 from build-system.requires Requirement satisfied: setuptools>=59.0 (installed: setuptools 80.10.2) Handling Cython>=3,<4 from build-system.requires Requirement satisfied: Cython>=3,<4 (installed: Cython 3.2.4) # pysam: Cython 3.2.4 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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 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' 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' # pysam: Cython 3.2.4 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 -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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 dist_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' 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' creating '/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam-0.24.0.dist-info' + cat /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-buildrequires + rm -rfv pysam-0.24.0.dist-info/ removed 'pysam-0.24.0.dist-info/licenses/AUTHORS' removed 'pysam-0.24.0.dist-info/licenses/COPYING' removed directory 'pysam-0.24.0.dist-info/licenses' removed 'pysam-0.24.0.dist-info/METADATA' removed 'pysam-0.24.0.dist-info/top_level.txt' removed directory 'pysam-0.24.0.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.xdI6hu + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.24.0 + export FORCE_CYTHON=1 + FORCE_CYTHON=1 + mkdir -p /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir Processing ./. Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) # pysam: Cython 3.2.4 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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 dist_info creating /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info writing /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info/dependency_links.txt writing top-level names to /builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/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 '/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir/pip-modern-metadata-49gou6bd/pysam-0.24.0.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: pysam Building wheel for pysam (pyproject.toml): started Running command Building wheel for pysam (pyproject.toml) # pysam: Cython 3.2.4 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-hardened-ld-errors -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed 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 build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 /usr/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # 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 simd.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 bdist_wheel running build running build_py creating build/lib.linux-aarch64-cpython-314/pysam copying pysam/config.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/version.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/utils.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/samtools.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/bcftools.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/__init__.py -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/Pileup.py -> build/lib.linux-aarch64-cpython-314/pysam creating build/lib.linux-aarch64-cpython-314/pysam/include copying pysam/include/__init__.py -> build/lib.linux-aarch64-cpython-314/pysam/include 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' 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/python3.14/site-packages/setuptools/command/build_py.py:215: _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/python3.14/site-packages/setuptools/command/build_py.py:215: _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/python3.14/site-packages/setuptools/command/build_py.py:215: _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/python3.14/site-packages/setuptools/command/build_py.py:215: _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/python3.14/site-packages/setuptools/command/build_py.py:215: _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/conftest_cstd.c -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/htslib_util.c -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/htslib_util.h -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcf.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcf.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcf.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbgzf.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libchtslib.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libchtslib.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libchtslib.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabix.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabix.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabix.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcutils.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcutils.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcutils.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcvcf.pxd -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcvcf.pyi -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/libcvcf.pyx -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/py.typed -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/version.h -> build/lib.linux-aarch64-cpython-314/pysam copying pysam/version.pyi -> build/lib.linux-aarch64-cpython-314/pysam creating build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/README -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_checksum.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_checksum.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_consensus_tab.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools creating build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-aarch64-cpython-314/pysam/include/samtools creating build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/README -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/edlib.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/edlib.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/edlib.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-aarch64-cpython-314/pysam/include/bcftools creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/README -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/bgzf_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/config.guess -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/config.sub -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/configure -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/fuzz_settings.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/header.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/header.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/region.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/simd.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4 creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib creating build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib running build_ext checking for gcc option to enable C99 features... creating build/temp.linux-aarch64-cpython-314/pysam 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 -fPIC -I/usr/include/python3.14 -c pysam/conftest_cstd.c -o build/temp.linux-aarch64-cpython-314/pysam/conftest_cstd.o gcc option to enable C99 features: none needed 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 kstring.c: In function ‘boyer_moore’: kstring.c:454:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 454 | return memchr(str, pat[0], n); | ^~~~~~ 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 faidx.c: In function ‘fai_path’: faidx.c:1042:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1042 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^~~~~~ 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 "1.23.1"' > 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 hts.c: In function ‘hts_open_format’: hts.c:941:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 941 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ hts.c: In function ‘hts_hopen’: hts.c:1477:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1477 | if ((cp = strchr(mode, ','))) { | ^ hts.c: In function ‘idx_find_and_load’: hts.c:4922:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4922 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ 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 sam.c: In function ‘sam_open_mode_opts’: sam.c:5235:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5235 | if ((opts = strchr(format, ','))) { | ^ 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 simd.o simd.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 vcf.c: In function ‘bcf_get_version’: vcf.c:167:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 167 | if (!(major = strstr(version, vcf))) { //bad format | ^ 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 cram/cram_decode.c: In function ‘cram_decode_seq’: cram/cram_decode.c:1245:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1245 | char *N = memchr(refp, 'N', frag_len); | ^~~~~~ 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 cram/cram_io.c: In function ‘refs_load_fai’: cram/cram_io.c:2561:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2561 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:5357:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5357 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ 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 simd.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 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/htslib_util.c -o build/temp.linux-aarch64-cpython-314/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libchtslib.c -o build/temp.linux-aarch64-cpython-314/pysam/libchtslib.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-hardened-ld-errors -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-314/pysam/htslib_util.o build/temp.linux-aarch64-cpython-314/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/simd.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-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-aarch64-cpython-314/pysam/libchtslib.cpython-314-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-314/samtools creating build/temp.linux-aarch64-cpython-314/samtools/lz4 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcsamtools.c -o build/temp.linux-aarch64-cpython-314/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_checksum.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_checksum.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_color.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_import.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_index.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_md.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_split.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_split.c.pysam.c: In function ‘prep_sam_file’: samtools/bam_split.c.pysam.c:381:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 381 | char *dirsep = strrchr(opts->merged_input_name, '/'); | ^~~~~~~ samtools/bam_split.c.pysam.c: In function ‘init’: samtools/bam_split.c.pysam.c:643:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 643 | char* dirsep = strrchr(opts->merged_input_name, '/'); | ^~~~~~~ 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bamtk.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bedcov.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/bedidx.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/coverage.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/cram_size.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/cut_target.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/dict.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/faidx.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/lz4/lz4.c -o build/temp.linux-aarch64-cpython-314/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/padding.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/phase.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/reference.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/reset.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/sam_utils.c.pysam.c: In function ‘auto_index’: samtools/sam_utils.c.pysam.c:124:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 124 | char *delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/sam_view.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/sample.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/samtools.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/stats.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-aarch64-cpython-314/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-aarch64-cpython-314/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-hardened-ld-errors -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-314/pysam/libcsamtools.o build/temp.linux-aarch64-cpython-314/samtools/amplicon_stats.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam2depth.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_addrprg.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_aux.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_cat.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_checksum.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_color.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_consensus.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_fastq.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_flags.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_import.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_index.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_lpileup.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_markdup.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_mate.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_md.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_plbuf.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_plcmd.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_quickcheck.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_reheader.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_rmdup.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_rmdupse.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_samples.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_sort.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_split.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bam_stat.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bamshuf.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bamtk.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bedcov.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/bedidx.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/consensus_pileup.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/coverage.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/cram_size.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/cut_target.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/dict.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/faidx.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/lz4/lz4.o build/temp.linux-aarch64-cpython-314/samtools/padding.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/phase.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/reference.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/reset.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/sam_opts.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/sam_utils.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/sam_view.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/sample.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/samtools.pysam.o build/temp.linux-aarch64-cpython-314/samtools/stats.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/stats_isize.c.pysam.o build/temp.linux-aarch64-cpython-314/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcsamtools.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-aarch64-cpython-314/bcftools 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/HMM.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/abuf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bam2bcf_edlib.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/bam_sample.c.pysam.c: In function ‘bam_smpl_add_bam’: bcftools/bam_sample.c.pysam.c:174:21: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 174 | char *eol = strchr(q + 3, '\n'); | ^~~~~~ 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bcftools.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/bin.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/ccall.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/cols.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/convert.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/csq.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/dist.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/edlib.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/em.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/extsort.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/filter.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/gff.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/hclust.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/kmin.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/main.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/mcall.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/prob1.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/regidx.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/tabix.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c bcftools/version.c.pysam.c -o build/temp.linux-aarch64-cpython-314/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/version.c.pysam.c: In function ‘init_index2’: bcftools/version.c.pysam.c:165:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 165 | char *delim = strstr(fname, HTS_IDX_DELIM); | ^~~~~~ 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcbcftools.c -o build/temp.linux-aarch64-cpython-314/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-hardened-ld-errors -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-314/bcftools/HMM.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/abuf.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_edlib.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bam_sample.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bcftools.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/bin.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/ccall.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/cols.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/consensus.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/convert.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/csq.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/dist.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/edlib.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/em.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/extsort.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/filter.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/gff.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/gvcf.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/hclust.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/kmin.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/main.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/mcall.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/mpileup.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/ploidy.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/prob1.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/read_consensus.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/regidx.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/reheader.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/smpl_ilist.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/str_finder.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/tabix.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/tsv2vcf.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfannotate.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfbuf.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfcall.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfcnv.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfconcat.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfconvert.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcffilter.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfhead.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfindex.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfisec.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfmerge.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfnorm.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfplugin.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfquery.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfroh.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfsom.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfsort.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfstats.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcfview.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/vcmp.c.pysam.o build/temp.linux-aarch64-cpython-314/bcftools/version.c.pysam.o build/temp.linux-aarch64-cpython-314/pysam/libcbcftools.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcbcftools.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcutils.c -o build/temp.linux-aarch64-cpython-314/pysam/libcutils.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-hardened-ld-errors -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-314/pysam/libcutils.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcsamtools.cpython-314-aarch64-linux-gnu -lcbcftools.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcutils.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcalignmentfile.c -o build/temp.linux-aarch64-cpython-314/pysam/libcalignmentfile.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-hardened-ld-errors -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-314/pysam/libcalignmentfile.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcalignmentfile.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcsamfile.c -o build/temp.linux-aarch64-cpython-314/pysam/libcsamfile.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-hardened-ld-errors -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-314/pysam/libcsamfile.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcsamfile.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcalignedsegment.c -o build/temp.linux-aarch64-cpython-314/pysam/libcalignedsegment.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-hardened-ld-errors -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-314/pysam/libcalignedsegment.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcalignedsegment.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libctabix.c -o build/temp.linux-aarch64-cpython-314/pysam/libctabix.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-hardened-ld-errors -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-314/pysam/libctabix.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libctabix.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcfaidx.c -o build/temp.linux-aarch64-cpython-314/pysam/libcfaidx.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-hardened-ld-errors -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-314/pysam/libcfaidx.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcfaidx.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcbcf.c -o build/temp.linux-aarch64-cpython-314/pysam/libcbcf.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-hardened-ld-errors -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-314/pysam/libcbcf.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcbcf.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcbgzf.c -o build/temp.linux-aarch64-cpython-314/pysam/libcbgzf.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-hardened-ld-errors -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-314/pysam/libcbgzf.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcbgzf.cpython-314-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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libctabixproxies.c -o build/temp.linux-aarch64-cpython-314/pysam/libctabixproxies.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-hardened-ld-errors -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-314/pysam/libctabixproxies.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libctabixproxies.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1084:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension 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 -fPIC -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/lz4 -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools -I/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -I/usr/include/python3.14 -c pysam/libcvcf.c -o build/temp.linux-aarch64-cpython-314/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:24994:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 24994 | __pyx_t_2 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 874, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:20674:10: note: ‘__pyx_v_qual’ was declared here 20674 | 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-hardened-ld-errors -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-314/pysam/libcvcf.o -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/pysam -L/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -Lbuild/lib.linux-aarch64-cpython-314/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-314-aarch64-linux-gnu -lcutils.cpython-314-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-314/pysam/libcvcf.cpython-314-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcvcf.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabixproxies.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbgzf.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcf.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcfaidx.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabix.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignedsegment.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamfile.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignmentfile.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcutils.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcftools.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamtools.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libchtslib.cpython-314-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/version.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/version.h -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/py.typed -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcvcf.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcvcf.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcvcf.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcutils.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcutils.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcutils.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabixproxies.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabixproxies.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabixproxies.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabix.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabix.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libctabix.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamtools.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamtools.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamtools.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamfile.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamfile.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcsamfile.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libchtslib.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libchtslib.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libchtslib.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcfaidx.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcfaidx.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcfaidx.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbgzf.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbgzf.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbgzf.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcftools.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcftools.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcftools.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcf.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcf.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcbcf.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignmentfile.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignmentfile.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignmentfile.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignedsegment.pyx -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignedsegment.pyi -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/libcalignedsegment.pxd -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/htslib_util.h -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/htslib_util.c -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/conftest_cstd.c -> build/bdist.linux-aarch64/wheel/./pysam creating build/bdist.linux-aarch64/wheel/pysam/include creating build/bdist.linux-aarch64/wheel/pysam/include/htslib creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/kroundup.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts_expr.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/config.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/os/rand.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/os/lzma_stub.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/os creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4/pkg.m4 -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/m4 creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/htscodecs creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/version.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/varint.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/utils.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/utils.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rle.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rle.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/permute.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/pack.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/pack.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/htscodecs/htscodecs creating build/bdist.linux-aarch64/wheel/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/string_alloc.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/string_alloc.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/pooled_alloc.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/pooled_alloc.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/os.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/open_trace_file.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/open_trace_file.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/misc.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/mFILE.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/mFILE.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_structs.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_stats.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_stats.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_samtools.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_io.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_io.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_index.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_index.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_external.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_encode.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_encode.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_decode.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_decode.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_codecs.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram_codecs.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/cram/cram.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/version.sh -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/vcfutils.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/vcf_sweep.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/vcf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/thread_pool.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/textutils.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/tbx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/synced_bcf_reader.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/simd.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/sam_mods.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/sam_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/sam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/region.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/regidx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/realn.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/probaln.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/plugin.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/multipart.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/md5.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/kstring.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/kfunc.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib_vars.mk -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib.pc.in -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htslib.mk -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs_external.mk -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/htscodecs_bundled.mk -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hts_time_funcs.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hts_os.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hts_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hts_expr.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hts.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hfile_s3.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hfile_libcurl.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hfile_gcs.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/hfile.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/header.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/header.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/fuzz_settings.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/faidx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/errmod.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/configure.ac -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/configure -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/config.sub -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/config.mk.in -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/config.h.in -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/config.guess -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/builddir_vars.mk.in -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/bgzf_internal.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/bgzf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/bcf_sr_sort.c -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/README -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/Makefile -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib copying build/lib.linux-aarch64-cpython-314/pysam/include/htslib/LICENSE -> build/bdist.linux-aarch64/wheel/./pysam/include/htslib creating build/bdist.linux-aarch64/wheel/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/config.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/version.sh -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/version.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/version.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcmp.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcmp.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcmp.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfview.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfview.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfstats.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfstats.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfsort.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfsort.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfsom.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfsom.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfroh.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfroh.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfquery.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfquery.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfplugin.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfplugin.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfnorm.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfnorm.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfmerge.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfmerge.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfisec.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfisec.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfindex.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfindex.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfhead.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfhead.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfgtcheck.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcffilter.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcffilter.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfconvert.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfconvert.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfconcat.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfconcat.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfcnv.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfcnv.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfcall.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfcall.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfbuf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfbuf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfannotate.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/vcfannotate.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/variantkey.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/utlist.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/tsv2vcf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/tsv2vcf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/tabix.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/tabix.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/str_finder.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/str_finder.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/str_finder.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/smpl_ilist.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/smpl_ilist.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/reheader.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/reheader.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/regidx.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/regidx.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/regidx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/read_consensus.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/read_consensus.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/read_consensus.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/rbuf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/prob1.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/prob1.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/prob1.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/ploidy.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/ploidy.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/ploidy.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/mw.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/mpileup.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/mpileup.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/mcall.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/mcall.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/main.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/main.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/kmin.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/kmin.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/kmin.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/kheap.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/hex.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/hclust.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/hclust.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/hclust.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gvcf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gvcf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gvcf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gff.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gff.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/gff.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/filter.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/filter.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/filter.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/extsort.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/extsort.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/extsort.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/em.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/em.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/edlib.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/edlib.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/edlib.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/dist.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/dist.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/dist.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/dbuf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/csq.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/csq.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/convert.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/convert.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/convert.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/consensus.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/consensus.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/cols.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/cols.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/cols.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/cigar_state.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/ccall.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/ccall.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/call.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bin.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bin.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bin.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bcftools.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bcftools.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam_sample.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam_sample.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_indel.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_iaux.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_edlib.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf_edlib.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/bam2bcf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/abuf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/abuf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/abuf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/README -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/LICENSE -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/HMM.h -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/HMM.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools copying build/lib.linux-aarch64-cpython-314/pysam/include/bcftools/HMM.c -> build/bdist.linux-aarch64/wheel/./pysam/include/bcftools creating build/bdist.linux-aarch64/wheel/pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/config.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools creating build/bdist.linux-aarch64/wheel/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4/lz4.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4/lz4.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4/lz4.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/lz4/LICENSE -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/version.sh -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/tmp_file.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/tmp_file.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/tmp_file.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/stats_isize.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/stats_isize.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/stats_isize.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/stats.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/stats.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/splaysort.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/samtools.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/samtools.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sample.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sample.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sample.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_view.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_view.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_utils.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_utils.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_utils.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_opts.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_opts.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/sam_opts.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/reset.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/reset.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/reference.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/reference.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/phase.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/phase.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/padding.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/padding.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/faidx.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/faidx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/dict.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/dict.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/cut_target.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/cut_target.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/cram_size.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/cram_size.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/coverage.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/coverage.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/consensus_pileup.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/consensus_pileup.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/consensus_pileup.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bedidx.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bedidx.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bedidx.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bedcov.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bedcov.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bamtk.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bamtk.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bamshuf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bamshuf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_stat.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_stat.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_split.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_split.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_sort.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_sort.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_samples.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_samples.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_rmdupse.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_rmdupse.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_rmdup.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_rmdup.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_reheader.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_reheader.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_quickcheck.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_quickcheck.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_plcmd.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_plcmd.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_plbuf.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_plbuf.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_md.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_md.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_mate.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_mate.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_markdup.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_markdup.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_lpileup.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_lpileup.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_index.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_index.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_import.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_import.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_flags.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_flags.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_fastq.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_fastq.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_consensus_tab.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_consensus.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_consensus.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_color.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_color.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_checksum.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_checksum.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_cat.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_cat.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_aux.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_aux.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_ampliconclip.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_ampliconclip.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_addrprg.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam_addrprg.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam2depth.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam2depth.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam.h -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/bam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/amplicon_stats.c.pysam.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/amplicon_stats.c -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/README -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/samtools/LICENSE -> build/bdist.linux-aarch64/wheel/./pysam/include/samtools copying build/lib.linux-aarch64-cpython-314/pysam/include/__init__.py -> build/bdist.linux-aarch64/wheel/./pysam/include copying build/lib.linux-aarch64-cpython-314/pysam/Pileup.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/__init__.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/bcftools.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/samtools.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/utils.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/version.py -> build/bdist.linux-aarch64/wheel/./pysam copying build/lib.linux-aarch64-cpython-314/pysam/config.py -> build/bdist.linux-aarch64/wheel/./pysam running install_egg_info Copying pysam.egg-info to build/bdist.linux-aarch64/wheel/./pysam-0.24.0-py3.14.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/pysam-0.24.0.dist-info/WHEEL creating '/builddir/.cache/pip/wheels/94/de/f2/c83d63087ea3268e9144a19e1136630ab8cbc2456784cbf9b9/tmp6m8js0y6/.tmp-0gl0manw/pysam-0.24.0-cp314-cp314-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'pysam/Pileup.py' adding 'pysam/__init__.py' adding 'pysam/bcftools.py' adding 'pysam/config.py' adding 'pysam/conftest_cstd.c' adding 'pysam/htslib_util.c' adding 'pysam/htslib_util.h' adding 'pysam/libcalignedsegment.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcalignedsegment.pxd' adding 'pysam/libcalignedsegment.pyi' adding 'pysam/libcalignedsegment.pyx' adding 'pysam/libcalignmentfile.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcalignmentfile.pxd' adding 'pysam/libcalignmentfile.pyi' adding 'pysam/libcalignmentfile.pyx' adding 'pysam/libcbcf.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcbcf.pxd' adding 'pysam/libcbcf.pyi' adding 'pysam/libcbcf.pyx' adding 'pysam/libcbcftools.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcbcftools.pxd' adding 'pysam/libcbcftools.pyi' adding 'pysam/libcbcftools.pyx' adding 'pysam/libcbgzf.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcbgzf.pxd' adding 'pysam/libcbgzf.pyi' adding 'pysam/libcbgzf.pyx' adding 'pysam/libcfaidx.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcfaidx.pxd' adding 'pysam/libcfaidx.pyi' adding 'pysam/libcfaidx.pyx' adding 'pysam/libchtslib.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libchtslib.pxd' adding 'pysam/libchtslib.pyi' adding 'pysam/libchtslib.pyx' adding 'pysam/libcsamfile.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcsamfile.pxd' adding 'pysam/libcsamfile.pyi' adding 'pysam/libcsamfile.pyx' adding 'pysam/libcsamtools.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcsamtools.pxd' adding 'pysam/libcsamtools.pyi' adding 'pysam/libcsamtools.pyx' adding 'pysam/libctabix.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libctabix.pxd' adding 'pysam/libctabix.pyi' adding 'pysam/libctabix.pyx' adding 'pysam/libctabixproxies.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libctabixproxies.pxd' adding 'pysam/libctabixproxies.pyi' adding 'pysam/libctabixproxies.pyx' adding 'pysam/libcutils.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcutils.pxd' adding 'pysam/libcutils.pyi' adding 'pysam/libcutils.pyx' adding 'pysam/libcvcf.cpython-314-aarch64-linux-gnu.so' adding 'pysam/libcvcf.pxd' adding 'pysam/libcvcf.pyi' adding 'pysam/libcvcf.pyx' adding 'pysam/py.typed' adding 'pysam/samtools.py' adding 'pysam/utils.py' adding 'pysam/version.h' adding 'pysam/version.py' adding 'pysam/version.pyi' adding 'pysam/include/__init__.py' adding 'pysam/include/bcftools/HMM.c' adding 'pysam/include/bcftools/HMM.c.pysam.c' adding 'pysam/include/bcftools/HMM.h' adding 'pysam/include/bcftools/LICENSE' adding 'pysam/include/bcftools/README' adding 'pysam/include/bcftools/abuf.c' adding 'pysam/include/bcftools/abuf.c.pysam.c' adding 'pysam/include/bcftools/abuf.h' adding 'pysam/include/bcftools/bam2bcf.c' adding 'pysam/include/bcftools/bam2bcf.c.pysam.c' adding 'pysam/include/bcftools/bam2bcf.h' adding 'pysam/include/bcftools/bam2bcf_edlib.c' adding 'pysam/include/bcftools/bam2bcf_edlib.c.pysam.c' adding 'pysam/include/bcftools/bam2bcf_iaux.c' adding 'pysam/include/bcftools/bam2bcf_iaux.c.pysam.c' adding 'pysam/include/bcftools/bam2bcf_indel.c' adding 'pysam/include/bcftools/bam2bcf_indel.c.pysam.c' adding 'pysam/include/bcftools/bam_sample.c' adding 'pysam/include/bcftools/bam_sample.c.pysam.c' adding 'pysam/include/bcftools/bam_sample.h' adding 'pysam/include/bcftools/bcftools.h' adding 'pysam/include/bcftools/bcftools.pysam.c' adding 'pysam/include/bcftools/bcftools.pysam.h' adding 'pysam/include/bcftools/bin.c' adding 'pysam/include/bcftools/bin.c.pysam.c' adding 'pysam/include/bcftools/bin.h' adding 'pysam/include/bcftools/call.h' adding 'pysam/include/bcftools/ccall.c' adding 'pysam/include/bcftools/ccall.c.pysam.c' adding 'pysam/include/bcftools/cigar_state.h' adding 'pysam/include/bcftools/cols.c' adding 'pysam/include/bcftools/cols.c.pysam.c' adding 'pysam/include/bcftools/cols.h' adding 'pysam/include/bcftools/config.h' adding 'pysam/include/bcftools/consensus.c' adding 'pysam/include/bcftools/consensus.c.pysam.c' adding 'pysam/include/bcftools/convert.c' adding 'pysam/include/bcftools/convert.c.pysam.c' adding 'pysam/include/bcftools/convert.h' adding 'pysam/include/bcftools/csq.c' adding 'pysam/include/bcftools/csq.c.pysam.c' adding 'pysam/include/bcftools/dbuf.h' adding 'pysam/include/bcftools/dist.c' adding 'pysam/include/bcftools/dist.c.pysam.c' adding 'pysam/include/bcftools/dist.h' adding 'pysam/include/bcftools/edlib.c' adding 'pysam/include/bcftools/edlib.c.pysam.c' adding 'pysam/include/bcftools/edlib.h' adding 'pysam/include/bcftools/em.c' adding 'pysam/include/bcftools/em.c.pysam.c' adding 'pysam/include/bcftools/extsort.c' adding 'pysam/include/bcftools/extsort.c.pysam.c' adding 'pysam/include/bcftools/extsort.h' adding 'pysam/include/bcftools/filter.c' adding 'pysam/include/bcftools/filter.c.pysam.c' adding 'pysam/include/bcftools/filter.h' adding 'pysam/include/bcftools/gff.c' adding 'pysam/include/bcftools/gff.c.pysam.c' adding 'pysam/include/bcftools/gff.h' adding 'pysam/include/bcftools/gvcf.c' adding 'pysam/include/bcftools/gvcf.c.pysam.c' adding 'pysam/include/bcftools/gvcf.h' adding 'pysam/include/bcftools/hclust.c' adding 'pysam/include/bcftools/hclust.c.pysam.c' adding 'pysam/include/bcftools/hclust.h' adding 'pysam/include/bcftools/hex.h' adding 'pysam/include/bcftools/khash_str2str.h' adding 'pysam/include/bcftools/kheap.h' adding 'pysam/include/bcftools/kmin.c' adding 'pysam/include/bcftools/kmin.c.pysam.c' adding 'pysam/include/bcftools/kmin.h' adding 'pysam/include/bcftools/main.c' adding 'pysam/include/bcftools/main.c.pysam.c' adding 'pysam/include/bcftools/mcall.c' adding 'pysam/include/bcftools/mcall.c.pysam.c' adding 'pysam/include/bcftools/mpileup.c' adding 'pysam/include/bcftools/mpileup.c.pysam.c' adding 'pysam/include/bcftools/mw.h' adding 'pysam/include/bcftools/ploidy.c' adding 'pysam/include/bcftools/ploidy.c.pysam.c' adding 'pysam/include/bcftools/ploidy.h' adding 'pysam/include/bcftools/prob1.c' adding 'pysam/include/bcftools/prob1.c.pysam.c' adding 'pysam/include/bcftools/prob1.h' adding 'pysam/include/bcftools/rbuf.h' adding 'pysam/include/bcftools/read_consensus.c' adding 'pysam/include/bcftools/read_consensus.c.pysam.c' adding 'pysam/include/bcftools/read_consensus.h' adding 'pysam/include/bcftools/regidx.c' adding 'pysam/include/bcftools/regidx.c.pysam.c' adding 'pysam/include/bcftools/regidx.h' adding 'pysam/include/bcftools/reheader.c' adding 'pysam/include/bcftools/reheader.c.pysam.c' adding 'pysam/include/bcftools/smpl_ilist.c' adding 'pysam/include/bcftools/smpl_ilist.c.pysam.c' adding 'pysam/include/bcftools/smpl_ilist.h' adding 'pysam/include/bcftools/str_finder.c' adding 'pysam/include/bcftools/str_finder.c.pysam.c' adding 'pysam/include/bcftools/str_finder.h' adding 'pysam/include/bcftools/tabix.c' adding 'pysam/include/bcftools/tabix.c.pysam.c' adding 'pysam/include/bcftools/tsv2vcf.c' adding 'pysam/include/bcftools/tsv2vcf.c.pysam.c' adding 'pysam/include/bcftools/tsv2vcf.h' adding 'pysam/include/bcftools/utlist.h' adding 'pysam/include/bcftools/variantkey.h' adding 'pysam/include/bcftools/vcfannotate.c' adding 'pysam/include/bcftools/vcfannotate.c.pysam.c' adding 'pysam/include/bcftools/vcfbuf.c' adding 'pysam/include/bcftools/vcfbuf.c.pysam.c' adding 'pysam/include/bcftools/vcfbuf.h' adding 'pysam/include/bcftools/vcfcall.c' adding 'pysam/include/bcftools/vcfcall.c.pysam.c' adding 'pysam/include/bcftools/vcfcnv.c' adding 'pysam/include/bcftools/vcfcnv.c.pysam.c' adding 'pysam/include/bcftools/vcfconcat.c' adding 'pysam/include/bcftools/vcfconcat.c.pysam.c' adding 'pysam/include/bcftools/vcfconvert.c' adding 'pysam/include/bcftools/vcfconvert.c.pysam.c' adding 'pysam/include/bcftools/vcffilter.c' adding 'pysam/include/bcftools/vcffilter.c.pysam.c' adding 'pysam/include/bcftools/vcfgtcheck.c' adding 'pysam/include/bcftools/vcfgtcheck.c.pysam.c' adding 'pysam/include/bcftools/vcfhead.c' adding 'pysam/include/bcftools/vcfhead.c.pysam.c' adding 'pysam/include/bcftools/vcfindex.c' adding 'pysam/include/bcftools/vcfindex.c.pysam.c' adding 'pysam/include/bcftools/vcfisec.c' adding 'pysam/include/bcftools/vcfisec.c.pysam.c' adding 'pysam/include/bcftools/vcfmerge.c' adding 'pysam/include/bcftools/vcfmerge.c.pysam.c' adding 'pysam/include/bcftools/vcfnorm.c' adding 'pysam/include/bcftools/vcfnorm.c.pysam.c' adding 'pysam/include/bcftools/vcfplugin.c' adding 'pysam/include/bcftools/vcfplugin.c.pysam.c' adding 'pysam/include/bcftools/vcfquery.c' adding 'pysam/include/bcftools/vcfquery.c.pysam.c' adding 'pysam/include/bcftools/vcfroh.c' adding 'pysam/include/bcftools/vcfroh.c.pysam.c' adding 'pysam/include/bcftools/vcfsom.c' adding 'pysam/include/bcftools/vcfsom.c.pysam.c' adding 'pysam/include/bcftools/vcfsort.c' adding 'pysam/include/bcftools/vcfsort.c.pysam.c' adding 'pysam/include/bcftools/vcfstats.c' adding 'pysam/include/bcftools/vcfstats.c.pysam.c' adding 'pysam/include/bcftools/vcfview.c' adding 'pysam/include/bcftools/vcfview.c.pysam.c' adding 'pysam/include/bcftools/vcmp.c' adding 'pysam/include/bcftools/vcmp.c.pysam.c' adding 'pysam/include/bcftools/vcmp.h' adding 'pysam/include/bcftools/version.c' adding 'pysam/include/bcftools/version.c.pysam.c' adding 'pysam/include/bcftools/version.sh' adding 'pysam/include/htslib/LICENSE' adding 'pysam/include/htslib/Makefile' adding 'pysam/include/htslib/README' adding 'pysam/include/htslib/bcf_sr_sort.c' adding 'pysam/include/htslib/bcf_sr_sort.h' adding 'pysam/include/htslib/bgzf.c' adding 'pysam/include/htslib/bgzf_internal.h' adding 'pysam/include/htslib/builddir_vars.mk.in' adding 'pysam/include/htslib/config.guess' adding 'pysam/include/htslib/config.h' adding 'pysam/include/htslib/config.h.in' adding 'pysam/include/htslib/config.mk.in' adding 'pysam/include/htslib/config.sub' adding 'pysam/include/htslib/configure' adding 'pysam/include/htslib/configure.ac' adding 'pysam/include/htslib/errmod.c' adding 'pysam/include/htslib/faidx.c' adding 'pysam/include/htslib/fuzz_settings.h' adding 'pysam/include/htslib/header.c' adding 'pysam/include/htslib/header.h' adding 'pysam/include/htslib/hfile.c' adding 'pysam/include/htslib/hfile_gcs.c' adding 'pysam/include/htslib/hfile_internal.h' adding 'pysam/include/htslib/hfile_libcurl.c' adding 'pysam/include/htslib/hfile_s3.c' adding 'pysam/include/htslib/hts.c' adding 'pysam/include/htslib/hts_expr.c' adding 'pysam/include/htslib/hts_internal.h' adding 'pysam/include/htslib/hts_os.c' adding 'pysam/include/htslib/hts_time_funcs.h' adding 'pysam/include/htslib/htscodecs_bundled.mk' adding 'pysam/include/htslib/htscodecs_external.mk' adding 'pysam/include/htslib/htslib.mk' adding 'pysam/include/htslib/htslib.pc.in' adding 'pysam/include/htslib/htslib_vars.mk' adding 'pysam/include/htslib/kfunc.c' adding 'pysam/include/htslib/kstring.c' adding 'pysam/include/htslib/md5.c' adding 'pysam/include/htslib/multipart.c' adding 'pysam/include/htslib/plugin.c' adding 'pysam/include/htslib/probaln.c' adding 'pysam/include/htslib/realn.c' adding 'pysam/include/htslib/regidx.c' adding 'pysam/include/htslib/region.c' adding 'pysam/include/htslib/sam.c' adding 'pysam/include/htslib/sam_internal.h' adding 'pysam/include/htslib/sam_mods.c' adding 'pysam/include/htslib/simd.c' adding 'pysam/include/htslib/synced_bcf_reader.c' adding 'pysam/include/htslib/tbx.c' adding 'pysam/include/htslib/textutils.c' adding 'pysam/include/htslib/textutils_internal.h' adding 'pysam/include/htslib/thread_pool.c' adding 'pysam/include/htslib/thread_pool_internal.h' adding 'pysam/include/htslib/vcf.c' adding 'pysam/include/htslib/vcf_sweep.c' adding 'pysam/include/htslib/vcfutils.c' adding 'pysam/include/htslib/version.sh' adding 'pysam/include/htslib/cram/cram.h' adding 'pysam/include/htslib/cram/cram_codecs.c' adding 'pysam/include/htslib/cram/cram_codecs.h' adding 'pysam/include/htslib/cram/cram_decode.c' adding 'pysam/include/htslib/cram/cram_decode.h' adding 'pysam/include/htslib/cram/cram_encode.c' adding 'pysam/include/htslib/cram/cram_encode.h' adding 'pysam/include/htslib/cram/cram_external.c' adding 'pysam/include/htslib/cram/cram_index.c' adding 'pysam/include/htslib/cram/cram_index.h' adding 'pysam/include/htslib/cram/cram_io.c' adding 'pysam/include/htslib/cram/cram_io.h' adding 'pysam/include/htslib/cram/cram_samtools.h' adding 'pysam/include/htslib/cram/cram_stats.c' adding 'pysam/include/htslib/cram/cram_stats.h' adding 'pysam/include/htslib/cram/cram_structs.h' adding 'pysam/include/htslib/cram/mFILE.c' adding 'pysam/include/htslib/cram/mFILE.h' adding 'pysam/include/htslib/cram/misc.h' adding 'pysam/include/htslib/cram/open_trace_file.c' adding 'pysam/include/htslib/cram/open_trace_file.h' adding 'pysam/include/htslib/cram/os.h' adding 'pysam/include/htslib/cram/pooled_alloc.c' adding 'pysam/include/htslib/cram/pooled_alloc.h' adding 'pysam/include/htslib/cram/string_alloc.c' adding 'pysam/include/htslib/cram/string_alloc.h' adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c' adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h' adding 'pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h' adding 'pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h' adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c' adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h' adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.c' adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.h' adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h' adding 'pysam/include/htslib/htscodecs/htscodecs/pack.c' adding 'pysam/include/htslib/htscodecs/htscodecs/pack.h' adding 'pysam/include/htslib/htscodecs/htscodecs/permute.h' adding 'pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_word.h' adding 'pysam/include/htslib/htscodecs/htscodecs/rle.c' adding 'pysam/include/htslib/htscodecs/htscodecs/rle.h' adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c' adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h' adding 'pysam/include/htslib/htscodecs/htscodecs/utils.c' adding 'pysam/include/htslib/htscodecs/htscodecs/utils.h' adding 'pysam/include/htslib/htscodecs/htscodecs/varint.h' adding 'pysam/include/htslib/htscodecs/htscodecs/varint2.h' adding 'pysam/include/htslib/htscodecs/htscodecs/version.h' adding 'pysam/include/htslib/htslib/bgzf.h' adding 'pysam/include/htslib/htslib/cram.h' adding 'pysam/include/htslib/htslib/faidx.h' adding 'pysam/include/htslib/htslib/hfile.h' adding 'pysam/include/htslib/htslib/hts.h' adding 'pysam/include/htslib/htslib/hts_defs.h' adding 'pysam/include/htslib/htslib/hts_endian.h' adding 'pysam/include/htslib/htslib/hts_expr.h' adding 'pysam/include/htslib/htslib/hts_log.h' adding 'pysam/include/htslib/htslib/hts_os.h' adding 'pysam/include/htslib/htslib/kbitset.h' adding 'pysam/include/htslib/htslib/kfunc.h' adding 'pysam/include/htslib/htslib/khash.h' adding 'pysam/include/htslib/htslib/khash_str2int.h' adding 'pysam/include/htslib/htslib/klist.h' adding 'pysam/include/htslib/htslib/knetfile.h' adding 'pysam/include/htslib/htslib/kroundup.h' adding 'pysam/include/htslib/htslib/kseq.h' adding 'pysam/include/htslib/htslib/ksort.h' adding 'pysam/include/htslib/htslib/kstring.h' adding 'pysam/include/htslib/htslib/regidx.h' adding 'pysam/include/htslib/htslib/sam.h' adding 'pysam/include/htslib/htslib/synced_bcf_reader.h' adding 'pysam/include/htslib/htslib/tbx.h' adding 'pysam/include/htslib/htslib/thread_pool.h' adding 'pysam/include/htslib/htslib/vcf.h' adding 'pysam/include/htslib/htslib/vcf_sweep.h' adding 'pysam/include/htslib/htslib/vcfutils.h' adding 'pysam/include/htslib/m4/hts_check_compile_flags_needed.m4' adding 'pysam/include/htslib/m4/hts_hide_dynamic_syms.m4' adding 'pysam/include/htslib/m4/hts_prog_cc_warnings.m4' adding 'pysam/include/htslib/m4/pkg.m4' adding 'pysam/include/htslib/os/lzma_stub.h' adding 'pysam/include/htslib/os/rand.c' adding 'pysam/include/samtools/LICENSE' adding 'pysam/include/samtools/README' adding 'pysam/include/samtools/amplicon_stats.c' adding 'pysam/include/samtools/amplicon_stats.c.pysam.c' adding 'pysam/include/samtools/bam.c' adding 'pysam/include/samtools/bam.c.pysam.c' adding 'pysam/include/samtools/bam.h' adding 'pysam/include/samtools/bam2depth.c' adding 'pysam/include/samtools/bam2depth.c.pysam.c' adding 'pysam/include/samtools/bam_addrprg.c' adding 'pysam/include/samtools/bam_addrprg.c.pysam.c' adding 'pysam/include/samtools/bam_ampliconclip.c' adding 'pysam/include/samtools/bam_ampliconclip.c.pysam.c' adding 'pysam/include/samtools/bam_ampliconclip.h' adding 'pysam/include/samtools/bam_aux.c' adding 'pysam/include/samtools/bam_aux.c.pysam.c' adding 'pysam/include/samtools/bam_cat.c' adding 'pysam/include/samtools/bam_cat.c.pysam.c' adding 'pysam/include/samtools/bam_checksum.c' adding 'pysam/include/samtools/bam_checksum.c.pysam.c' adding 'pysam/include/samtools/bam_color.c' adding 'pysam/include/samtools/bam_color.c.pysam.c' adding 'pysam/include/samtools/bam_consensus.c' adding 'pysam/include/samtools/bam_consensus.c.pysam.c' adding 'pysam/include/samtools/bam_consensus_tab.h' adding 'pysam/include/samtools/bam_fastq.c' adding 'pysam/include/samtools/bam_fastq.c.pysam.c' adding 'pysam/include/samtools/bam_flags.c' adding 'pysam/include/samtools/bam_flags.c.pysam.c' adding 'pysam/include/samtools/bam_import.c' adding 'pysam/include/samtools/bam_import.c.pysam.c' adding 'pysam/include/samtools/bam_index.c' adding 'pysam/include/samtools/bam_index.c.pysam.c' adding 'pysam/include/samtools/bam_lpileup.c' adding 'pysam/include/samtools/bam_lpileup.c.pysam.c' adding 'pysam/include/samtools/bam_lpileup.h' adding 'pysam/include/samtools/bam_markdup.c' adding 'pysam/include/samtools/bam_markdup.c.pysam.c' adding 'pysam/include/samtools/bam_mate.c' adding 'pysam/include/samtools/bam_mate.c.pysam.c' adding 'pysam/include/samtools/bam_md.c' adding 'pysam/include/samtools/bam_md.c.pysam.c' adding 'pysam/include/samtools/bam_plbuf.c' adding 'pysam/include/samtools/bam_plbuf.c.pysam.c' adding 'pysam/include/samtools/bam_plbuf.h' adding 'pysam/include/samtools/bam_plcmd.c' adding 'pysam/include/samtools/bam_plcmd.c.pysam.c' adding 'pysam/include/samtools/bam_quickcheck.c' adding 'pysam/include/samtools/bam_quickcheck.c.pysam.c' adding 'pysam/include/samtools/bam_reheader.c' adding 'pysam/include/samtools/bam_reheader.c.pysam.c' adding 'pysam/include/samtools/bam_rmdup.c' adding 'pysam/include/samtools/bam_rmdup.c.pysam.c' adding 'pysam/include/samtools/bam_rmdupse.c' adding 'pysam/include/samtools/bam_rmdupse.c.pysam.c' adding 'pysam/include/samtools/bam_samples.c' adding 'pysam/include/samtools/bam_samples.c.pysam.c' adding 'pysam/include/samtools/bam_sort.c' adding 'pysam/include/samtools/bam_sort.c.pysam.c' adding 'pysam/include/samtools/bam_split.c' adding 'pysam/include/samtools/bam_split.c.pysam.c' adding 'pysam/include/samtools/bam_stat.c' adding 'pysam/include/samtools/bam_stat.c.pysam.c' adding 'pysam/include/samtools/bamshuf.c' adding 'pysam/include/samtools/bamshuf.c.pysam.c' adding 'pysam/include/samtools/bamtk.c' adding 'pysam/include/samtools/bamtk.c.pysam.c' adding 'pysam/include/samtools/bedcov.c' adding 'pysam/include/samtools/bedcov.c.pysam.c' adding 'pysam/include/samtools/bedidx.c' adding 'pysam/include/samtools/bedidx.c.pysam.c' adding 'pysam/include/samtools/bedidx.h' adding 'pysam/include/samtools/config.h' adding 'pysam/include/samtools/consensus_pileup.c' adding 'pysam/include/samtools/consensus_pileup.c.pysam.c' adding 'pysam/include/samtools/consensus_pileup.h' adding 'pysam/include/samtools/coverage.c' adding 'pysam/include/samtools/coverage.c.pysam.c' adding 'pysam/include/samtools/cram_size.c' adding 'pysam/include/samtools/cram_size.c.pysam.c' adding 'pysam/include/samtools/cut_target.c' adding 'pysam/include/samtools/cut_target.c.pysam.c' adding 'pysam/include/samtools/dict.c' adding 'pysam/include/samtools/dict.c.pysam.c' adding 'pysam/include/samtools/faidx.c' adding 'pysam/include/samtools/faidx.c.pysam.c' adding 'pysam/include/samtools/padding.c' adding 'pysam/include/samtools/padding.c.pysam.c' adding 'pysam/include/samtools/phase.c' adding 'pysam/include/samtools/phase.c.pysam.c' adding 'pysam/include/samtools/reference.c' adding 'pysam/include/samtools/reference.c.pysam.c' adding 'pysam/include/samtools/reset.c' adding 'pysam/include/samtools/reset.c.pysam.c' adding 'pysam/include/samtools/sam_opts.c' adding 'pysam/include/samtools/sam_opts.c.pysam.c' adding 'pysam/include/samtools/sam_opts.h' adding 'pysam/include/samtools/sam_utils.c' adding 'pysam/include/samtools/sam_utils.c.pysam.c' adding 'pysam/include/samtools/sam_utils.h' adding 'pysam/include/samtools/sam_view.c' adding 'pysam/include/samtools/sam_view.c.pysam.c' adding 'pysam/include/samtools/sample.c' adding 'pysam/include/samtools/sample.c.pysam.c' adding 'pysam/include/samtools/sample.h' adding 'pysam/include/samtools/samtools.h' adding 'pysam/include/samtools/samtools.pysam.c' adding 'pysam/include/samtools/samtools.pysam.h' adding 'pysam/include/samtools/splaysort.h' adding 'pysam/include/samtools/stats.c' adding 'pysam/include/samtools/stats.c.pysam.c' adding 'pysam/include/samtools/stats_isize.c' adding 'pysam/include/samtools/stats_isize.c.pysam.c' adding 'pysam/include/samtools/stats_isize.h' adding 'pysam/include/samtools/tmp_file.c' adding 'pysam/include/samtools/tmp_file.c.pysam.c' adding 'pysam/include/samtools/tmp_file.h' adding 'pysam/include/samtools/version.sh' adding 'pysam/include/samtools/lz4/LICENSE' adding 'pysam/include/samtools/lz4/lz4.c' adding 'pysam/include/samtools/lz4/lz4.c.pysam.c' adding 'pysam/include/samtools/lz4/lz4.h' adding 'pysam-0.24.0.dist-info/licenses/AUTHORS' adding 'pysam-0.24.0.dist-info/licenses/COPYING' adding 'pysam-0.24.0.dist-info/METADATA' adding 'pysam-0.24.0.dist-info/WHEEL' adding 'pysam-0.24.0.dist-info/top_level.txt' adding 'pysam-0.24.0.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Building wheel for pysam (pyproject.toml): finished with status 'done' Created wheel for pysam: filename=pysam-0.24.0-cp314-cp314-linux_aarch64.whl size=16888481 sha256=35a4ec34a1083bb9c1b5ed8f5acce299bd784bb91f2c8fe4a50e55152ebea0bb Stored in directory: /builddir/.cache/pip/wheels/94/de/f2/c83d63087ea3268e9144a19e1136630ab8cbc2456784cbf9b9 Successfully built pysam ++ echo /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/build/lib.linux-aarch64-cpython-314 + PYTHONPATH=/builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/build/lib.linux-aarch64-cpython-314 + sphinx-build-3 doc html Running Sphinx v9.1.0 loading translations [en]... done 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 'python' from https://docs.python.org/3.14/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.14/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.14/objects.inv (Caused by NameResolutionError("HTTPSConnection(host='docs.python.org', port=443): 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... Writing evaluated template result to /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/html/_static/language_data.js Writing evaluated template result to /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/html/_static/documentation_options.js Writing evaluated template result to /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/html/_static/basic.css Writing evaluated template result to /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/html/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: 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.xxjcVh + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + '[' /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/python-pysam-0.24.0-build + mkdir /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.24.0 ++ ls /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir/pysam-0.24.0-cp314-cp314-linux_aarch64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=pysam==0.24.0 + '[' -z pysam==0.24.0 ']' + TMPDIR=/builddir/build/BUILD/python-pysam-0.24.0-build/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir pysam==0.24.0 Using pip 26.0.1 from /usr/lib/python3.14/site-packages/pip (python 3.14) Looking in links: /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir Processing /builddir/build/BUILD/python-pysam-0.24.0-build/pyproject-wheeldir/pysam-0.24.0-cp314-cp314-linux_aarch64.whl Installing collected packages: pysam Successfully installed pysam-0.24.0 + '[' -d /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/bin ']' + rm -f /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib/python3.14/site-packages ']' + '[' /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages '!=' /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib/python3.14/site-packages ']' + '[' -d /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages ']' + site_dirs+=("/usr/lib64/python3.14/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT$site_dir/*.dist-info + echo '%ghost %dir /usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT --record /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/RECORD --output /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-record + rm -fv /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/RECORD removed '/builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/RECORD' + rm -fv /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/REQUESTED removed '/builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam-0.24.0.dist-info/REQUESTED' + '[' -f /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-dep-overrides ']' ++ wc -l /builddir/build/BUILD/python-pysam-0.24.0-build/python-pysam-0.24.0-1.fc45.aarch64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + rm /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcbcf.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libchtslib.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libctabix.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcutils.pyx /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/conftest_cstd.c /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/htslib_util.c + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.24.0-1.fc45 --unique-debug-suffix -0.24.0-1.fc45.aarch64 --unique-debug-src-base python-pysam-0.24.0-1.fc45.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0 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-0.24.0-1.fc45.aarch64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/htslib/config.sub from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/htslib/config.guess from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.14/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.14 using python3.14 Bytecompiling .py files below /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14 using python3.14 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j4 /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/version.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/config.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/samtools.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/bcftools.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/utils.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/include/__pycache__/__init__.cpython-314.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/Pileup.cpython-314.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/lib64/python3.14/site-packages/pysam/__pycache__/Pileup.cpython-314.pyc: replacing with normalized version Scanned 41 directories and 798 files, processed 9 inodes, 9 modified (2 replaced + 7 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr Scanned 40 directories and 798 files, considered 798 files, read 18 files, linked 3 files, 0 errors sum of sizes of linked files: 77 bytes Reading /builddir/build/BUILD/python-pysam-0.24.0-build/SPECPARTS/rpm-debuginfo.specpart Processing files: python3-pysam-0.24.0-1.fc45.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FvUuXf + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + DOCDIR=/builddir/build/BUILD/python-pysam-0.24.0-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-0.24.0-build/BUILDROOT/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/README.rst /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.MCHDhx + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + LICENSEDIR=/builddir/build/BUILD/python-pysam-0.24.0-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-0.24.0-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/COPYING /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/bcftools/LICENSE /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/htslib/LICENSE /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/samtools/LICENSE /builddir/build/BUILD/python-pysam-0.24.0-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) = 1.23.1 bundled(htslib) = 1.23.1 bundled(samtools) = 1.23.1 libcalignedsegment.cpython-314-aarch64-linux-gnu.so()(64bit) libcalignmentfile.cpython-314-aarch64-linux-gnu.so()(64bit) libcbcf.cpython-314-aarch64-linux-gnu.so()(64bit) libcbcftools.cpython-314-aarch64-linux-gnu.so()(64bit) libcbgzf.cpython-314-aarch64-linux-gnu.so()(64bit) libcfaidx.cpython-314-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-314-aarch64-linux-gnu.so()(64bit) libcsamfile.cpython-314-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-314-aarch64-linux-gnu.so()(64bit) libctabix.cpython-314-aarch64-linux-gnu.so()(64bit) libctabixproxies.cpython-314-aarch64-linux-gnu.so()(64bit) libcutils.cpython-314-aarch64-linux-gnu.so()(64bit) libcvcf.cpython-314-aarch64-linux-gnu.so()(64bit) python-pysam = 0.24.0-1.fc45 python3-pysam = 0.24.0-1.fc45 python3-pysam(aarch-64) = 0.24.0-1.fc45 python3.14-pysam = 0.24.0-1.fc45 python3.14dist(pysam) = 0.24 python3dist(pysam) = 0.24 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-314-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-314-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-314-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) libm.so.6(GLIBC_2.43)(64bit) libz.so.1()(64bit) python(abi) = 3.14 rtld(GNU_HASH) Processing files: python3-pysam-devel-0.24.0-1.fc45.aarch64 Provides: python-pysam-devel = 0.24.0-1.fc45 python3-pysam-devel = 0.24.0-1.fc45 python3-pysam-devel(aarch-64) = 0.24.0-1.fc45 python3.14-pysam-devel = 0.24.0-1.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh python(abi) = 3.14 Processing files: python-pysam-doc-0.24.0-1.fc45.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.l5YwUF + umask 022 + cd /builddir/build/BUILD/python-pysam-0.24.0-build + cd pysam-0.24.0 + DOCDIR=/builddir/build/BUILD/python-pysam-0.24.0-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-0.24.0-build/BUILDROOT/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/python-pysam-0.24.0-build/pysam-0.24.0/html /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.24.0-1.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.24.0-1.fc45.aarch64 Provides: python-pysam-debugsource = 0.24.0-1.fc45 python-pysam-debugsource(aarch-64) = 0.24.0-1.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.24.0-1.fc45.aarch64 Provides: debuginfo(build-id) = 01d2d5214f69769270ced2190ae8830ff8c5a88e debuginfo(build-id) = 05bd44abc74458ae644ac6bd63525ac6df81d672 debuginfo(build-id) = 0f2b8be917c4cd6281011e3b4bfe7a86cb73838e debuginfo(build-id) = 138f2cbd2001cdc12fd2e965812ae9e4f554a3a1 debuginfo(build-id) = 1e44821e419c5cd7c9f8f9a941fe7a0f2c30a6d4 debuginfo(build-id) = 253e8c5ff58df60b1d91f0bbe9511887445477e3 debuginfo(build-id) = 2d620641e8834fc9558857793c4f213de3e0e464 debuginfo(build-id) = 61025c9436ed5003293932c8e4c3a4e672299d3d debuginfo(build-id) = a4a5cc41253169b4f51fb7996570c7bf0f9fd209 debuginfo(build-id) = c20d61b3f1449a45015a66658b7ce894c3a9413c debuginfo(build-id) = cee26bed6781ffcf785ee0d13bd04c108ae86085 debuginfo(build-id) = f426860351936cfb3fad6c019b43138b10cc1562 debuginfo(build-id) = f7546917fab5a75b75f57808feebdd3c8a24eef6 libcalignedsegment.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcalignmentfile.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcbcf.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcbcftools.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcbgzf.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcfaidx.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libchtslib.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcsamfile.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcsamtools.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libctabix.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libctabixproxies.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcutils.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) libcvcf.cpython-314-aarch64-linux-gnu.so-0.24.0-1.fc45.aarch64.debug()(64bit) python-pysam-debuginfo = 0.24.0-1.fc45 python3-pysam-debuginfo = 0.24.0-1.fc45 python3-pysam-debuginfo(aarch-64) = 0.24.0-1.fc45 python3.14-pysam-debuginfo = 0.24.0-1.fc45 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) = 0.24.0-1.fc45 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/python-pysam-0.24.0-build/BUILDROOT Wrote: /builddir/build/SRPMS/python-pysam-0.24.0-1.fc45.src.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.24.0-1.fc45.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.24.0-1.fc45.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.24.0-1.fc45.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.24.0-1.fc45.aarch64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.24.0-1.fc45.aarch64.rpm 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-0.24.0-1.fc45.src.rpm Finish: build phase for python-pysam-0.24.0-1.fc45.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1778317779.858557/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.24.0-1.fc45.src.rpm) Config(child) 5 minutes 39 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python3-pysam", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "aarch64" }, { "name": "python-pysam", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "src" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "aarch64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "aarch64" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "aarch64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.24.0", "release": "1.fc45", "arch": "noarch" } ] } RPMResults finished