Warning: Permanently added '54.87.133.126' (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/6407839-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64 Version: 0.69 PID: 5712 Logging PID: 5713 Task: {'appstream': False, 'background': True, 'build_id': 6407839, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.21.0-2', 'project_dirname': 'zlib-ng-compat-mpb', 'project_name': 'zlib-ng-compat-mpb', 'project_owner': 'tuliom', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/tuliom/zlib-ng-compat-mpb/fedora-rawhide-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'tuliom/zlib-ng-compat-mpb--tuliom', 'source_json': {}, 'source_type': None, 'submitter': 'tuliom', 'tags': [], 'task_id': '6407839-fedora-rawhide-aarch64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam'... Running: git checkout df6b1de2eecf9ffcb551247d0ec58aa16cf5b345 -- cmd: ['git', 'checkout', 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam rc: 0 stdout: stderr: Note: switching to 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345'. 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 df6b1de automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/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-0.21.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o pysam-0.21.0.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/tuliom/zlib-ng-compat-mpb/python-pysam/pysam-0.21.0.tar.gz/md5/dca7fb36d2cf69ef887fe05ddd726998/pysam-0.21.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 3957k 100 3957k 0 0 61.1M 0 --:--:-- --:--:-- --:--:-- 61.3M INFO: Reading stdout from command: md5sum pysam-0.21.0.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1694965618.485673 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.1 starting (python version = 3.11.3, NVR = mock-5.1-1.fc38)... 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-q0omb0sp/python-pysam/python-pysam.spec) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 5.1 INFO: Mock Version: 5.1 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1694965618.485673/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1694965618.485673/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/e5f044ed8989be9cd40b2c2f59c88ac61d88bd9a229f7883760df7f5fca6dba7/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/e5f044ed8989be9cd40b2c2f59c88ac61d88bd9a229f7883760df7f5fca6dba7/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 43 MB/s | 2.0 MB 00:00 fedora 49 MB/s | 69 MB 00:01 Package python3-dnf-4.16.2-4.fc40.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.2-1.fc39 fedora 293 k Installing dependencies: dbus-libs aarch64 1:1.14.10-1.fc40 fedora 156 k python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k python3-dbus aarch64 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd aarch64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.1 M Installed size: 4.6 M Downloading Packages: (1/7): python3-dbus-1.3.2-4.fc39.aarch64.rpm 7.0 MB/s | 157 kB 00:00 (2/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 14 MB/s | 355 kB 00:00 (3/7): python3-dnf-plugins-core-4.4.2-1.fc39.no 28 MB/s | 293 kB 00:00 (4/7): python3-six-1.16.0-12.fc39.noarch.rpm 3.3 MB/s | 41 kB 00:00 (5/7): python3-distro-1.8.0-6.fc39.noarch.rpm 1.6 MB/s | 49 kB 00:00 (6/7): python3-systemd-235-5.fc39.aarch64.rpm 13 MB/s | 107 kB 00:00 (7/7): dbus-libs-1.14.10-1.fc40.aarch64.rpm 2.6 MB/s | 156 kB 00:00 -------------------------------------------------------------------------------- Total 10 MB/s | 1.1 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.aarch64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc40.aarch64 5/7 Installing : python3-dbus-1.3.2-4.fc39.aarch64 6/7 Installing : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7 Verifying : dbus-libs-1:1.14.10-1.fc40.aarch64 1/7 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7 Verifying : python3-dbus-1.3.2-4.fc39.aarch64 3/7 Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7 Verifying : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 5/7 Verifying : python3-six-1.16.0-12.fc39.noarch 6/7 Verifying : python3-systemd-235-5.fc39.aarch64 7/7 Installed: dbus-libs-1:1.14.10-1.fc40.aarch64 python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.aarch64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.2-1.fc39.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.aarch64 Complete! Finish(bootstrap): installing dnf tooling 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-aarch64-1694965618.485673/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 dnf detected and used (direct choice) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 36 MB/s | 2.0 MB 00:00 fedora 46 MB/s | 69 MB 00:01 Last metadata expiration check: 0:00:01 ago on Sun Sep 17 15:47:29 2023. Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash aarch64 5.2.15-5.fc39 fedora 1.8 M bzip2 aarch64 1.0.8-16.fc39 fedora 52 k coreutils aarch64 9.4-1.fc40 fedora 1.2 M cpio aarch64 2.14-4.fc39 fedora 277 k diffutils aarch64 3.10-3.fc39 fedora 396 k fedora-release-common noarch 40-0.7 fedora 18 k findutils aarch64 1:4.9.0-6.fc40 fedora 495 k gawk aarch64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack aarch64 2.38.9000-8.fc40 copr_base 73 k grep aarch64 3.11-5.fc40 fedora 296 k gzip aarch64 1.12-6.fc39 fedora 164 k info aarch64 7.0.3-3.fc39 fedora 179 k patch aarch64 2.7.6-22.fc39 fedora 123 k redhat-rpm-config noarch 270-1.fc40 copr_base 74 k rpm-build aarch64 4.18.99-1.fc40 fedora 79 k sed aarch64 4.8-14.fc39 fedora 304 k shadow-utils aarch64 2:4.14.0-1.fc40 fedora 1.3 M tar aarch64 2:1.35-2.fc40 fedora 854 k unzip aarch64 6.0-62.fc39 fedora 183 k util-linux aarch64 2.39.2-1.fc40 fedora 1.2 M which aarch64 2.21-40.fc39 fedora 42 k xz aarch64 5.4.4-1.fc39 fedora 556 k Installing dependencies: alternatives aarch64 1.25-1.fc39 fedora 38 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs aarch64 3.1.2-4.fc40 fedora 118 k authselect aarch64 1.4.2-3.fc39 fedora 144 k authselect-libs aarch64 1.4.2-3.fc39 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils aarch64 2.41-5.fc40 fedora 6.7 M binutils-gold aarch64 2.41-5.fc40 fedora 948 k bzip2-libs aarch64 1.0.8-16.fc39 fedora 43 k ca-certificates noarch 2023.2.60_v7.0.306-3.fc40 fedora 837 k coreutils-common aarch64 9.4-1.fc40 fedora 2.1 M cracklib aarch64 2.9.11-2.fc40 copr_base 84 k crypto-policies noarch 20230731-1.git5ed06e0.fc39 fedora 99 k curl aarch64 8.3.0-1.fc40 copr_base 350 k cyrus-sasl-lib aarch64 2.1.28-11.fc39 fedora 781 k debugedit aarch64 5.0-10.fc39 fedora 77 k dwz aarch64 0.15-3.fc39 fedora 136 k ed aarch64 1.19-4.fc39 fedora 78 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils aarch64 0.189-6.fc40 fedora 539 k elfutils-debuginfod-client aarch64 0.189-6.fc40 fedora 38 k elfutils-default-yama-scope noarch 0.189-6.fc40 fedora 13 k elfutils-libelf aarch64 0.189-6.fc40 fedora 194 k elfutils-libs aarch64 0.189-6.fc40 fedora 258 k fedora-gpg-keys noarch 40-0.1 fedora 130 k fedora-release noarch 40-0.7 fedora 8.0 k fedora-release-identity-basic noarch 40-0.7 fedora 8.8 k fedora-repos noarch 40-0.1 fedora 9.4 k fedora-repos-rawhide noarch 40-0.1 fedora 9.0 k file aarch64 5.45-1.fc40 copr_base 50 k file-libs aarch64 5.45-1.fc40 copr_base 762 k filesystem aarch64 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k forge-srpm-macros noarch 0.1.0-1.fc40 fedora 18 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal aarch64 13.2-8.fc40 fedora 3.8 M gdbm-libs aarch64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc aarch64 2.38.9000-8.fc40 copr_base 1.7 M glibc-common aarch64 2.38.9000-8.fc40 copr_base 346 k glibc-gconv-extra aarch64 2.38.9000-8.fc40 copr_base 2.0 M gmp aarch64 1:6.2.1-5.fc39 fedora 266 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.2.0-7.fc40 fedora 27 k jansson aarch64 2.13.1-7.fc39 fedora 46 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs aarch64 1.6.1-7.fc39 fedora 31 k krb5-libs aarch64 1.21.2-1.fc40 fedora 772 k libacl aarch64 2.3.1-9.fc40 fedora 23 k libarchive aarch64 3.7.2-1.fc40 fedora 402 k libattr aarch64 2.5.1-9.fc40 fedora 18 k libblkid aarch64 2.39.2-1.fc40 fedora 115 k libbrotli aarch64 1.1.0-1.fc40 fedora 344 k libcap aarch64 2.48-7.fc39 fedora 68 k libcap-ng aarch64 0.8.3-8.fc40 fedora 32 k libcom_err aarch64 1.47.0-2.fc39 fedora 26 k libcurl aarch64 8.3.0-1.fc40 copr_base 337 k libdb aarch64 5.3.28-58.fc40 copr_base 735 k libeconf aarch64 0.5.2-1.fc40 fedora 30 k libevent aarch64 2.1.12-9.fc39 fedora 254 k libfdisk aarch64 2.39.2-1.fc40 fedora 158 k libffi aarch64 3.4.4-4.fc39 fedora 38 k libgcc aarch64 13.2.1-1.fc40 copr_base 94 k libgomp aarch64 13.2.1-1.fc40 copr_base 311 k libidn2 aarch64 2.3.4-3.fc39 fedora 118 k libmount aarch64 2.39.2-1.fc40 fedora 153 k libnghttp2 aarch64 1.56.0-1.fc40 fedora 75 k libnsl2 aarch64 2.0.0-6.fc39 fedora 30 k libpkgconf aarch64 1.9.5-2.fc39 fedora 38 k libpsl aarch64 0.21.2-4.fc39 fedora 63 k libpwquality aarch64 1.4.5-6.fc39 fedora 120 k libselinux aarch64 3.5-5.fc39 fedora 86 k libsemanage aarch64 3.5-4.fc39 fedora 117 k libsepol aarch64 3.5-2.fc39 fedora 311 k libsigsegv aarch64 2.14-5.fc39 fedora 27 k libsmartcols aarch64 2.39.2-1.fc40 fedora 65 k libssh aarch64 0.10.5-2.fc39 fedora 212 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ aarch64 13.2.1-1.fc40 copr_base 810 k libtasn1 aarch64 4.19.0-3.fc39 fedora 73 k libtirpc aarch64 1.3.3-1.rc2.fc39 fedora 95 k libunistring aarch64 1.1-5.fc40 fedora 540 k libutempter aarch64 1.2.1-10.fc39 fedora 27 k libuuid aarch64 2.39.2-1.fc40 fedora 28 k libverto aarch64 0.3.2-6.fc39 fedora 21 k libxcrypt aarch64 4.4.36-2.fc39 fedora 123 k libxml2 aarch64 2.11.5-1.fc40 copr_base 687 k libzstd aarch64 1.5.5-4.fc40 copr_base 281 k lua-libs aarch64 5.4.6-3.fc39 fedora 131 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs aarch64 1.9.4-4.fc39 fedora 68 k mpfr aarch64 4.2.0-3.fc39 fedora 319 k ncurses-base noarch 6.4-7.20230520.fc40 fedora 88 k ncurses-libs aarch64 6.4-7.20230520.fc40 fedora 326 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap aarch64 2.6.6-1.fc39 fedora 251 k openssl-libs aarch64 1:3.1.1-4.fc40 copr_base 2.0 M p11-kit aarch64 0.25.0-2.fc39 fedora 481 k p11-kit-trust aarch64 0.25.0-2.fc39 fedora 140 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam aarch64 1.5.3-2.fc39 fedora 558 k pam-libs aarch64 1.5.3-2.fc39 fedora 58 k pcre2 aarch64 10.42-1.fc39.2 fedora 219 k pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf aarch64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config aarch64 1.9.5-2.fc39 fedora 9.6 k popt aarch64 1.19-3.fc39 fedora 66 k publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k pyproject-srpm-macros noarch 1.9.0-2.fc39 fedora 14 k python-srpm-macros noarch 3.12-4.fc40 fedora 25 k qt5-srpm-macros noarch 5.15.10-2.fc39 fedora 8.3 k qt6-srpm-macros noarch 6.5.2-2.fc39 fedora 9.2 k readline aarch64 8.2-4.fc39 fedora 211 k rpm aarch64 4.18.99-1.fc40 fedora 537 k rpm-build-libs aarch64 4.18.99-1.fc40 fedora 92 k rpm-libs aarch64 4.18.99-1.fc40 fedora 305 k rpm-sequoia aarch64 1.5.0-1.fc40 fedora 842 k rust-srpm-macros noarch 24-5.fc40 fedora 12 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs aarch64 3.43.1-1.fc40 fedora 679 k systemd-libs aarch64 254.1-2.fc40 fedora 668 k tzdata noarch 2023c-3.fc40 fedora 718 k util-linux-core aarch64 2.39.2-1.fc40 fedora 490 k xxhash-libs aarch64 0.8.2-1.fc39 fedora 35 k xz-libs aarch64 5.4.4-1.fc39 fedora 106 k zip aarch64 3.0-38.fc39 fedora 262 k zlib-ng-compat aarch64 2.1.3-3.fc40 copr_base 68 k zstd aarch64 1.5.5-4.fc40 copr_base 446 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 153 Packages Total download size: 53 M Installed size: 304 M Downloading Packages: (1/153): cracklib-2.9.11-2.fc40.aarch64.rpm 5.0 MB/s | 84 kB 00:00 (2/153): curl-8.3.0-1.fc40.aarch64.rpm 19 MB/s | 350 kB 00:00 (3/153): file-5.45-1.fc40.aarch64.rpm 2.6 MB/s | 50 kB 00:00 (4/153): file-libs-5.45-1.fc40.aarch64.rpm 124 MB/s | 762 kB 00:00 (5/153): glibc-common-2.38.9000-8.fc40.aarch64. 85 MB/s | 346 kB 00:00 (6/153): glibc-2.38.9000-8.fc40.aarch64.rpm 193 MB/s | 1.7 MB 00:00 (7/153): glibc-minimal-langpack-2.38.9000-8.fc4 24 MB/s | 73 kB 00:00 (8/153): glibc-gconv-extra-2.38.9000-8.fc40.aar 196 MB/s | 2.0 MB 00:00 (9/153): libcurl-8.3.0-1.fc40.aarch64.rpm 64 MB/s | 337 kB 00:00 (10/153): libdb-5.3.28-58.fc40.aarch64.rpm 122 MB/s | 735 kB 00:00 (11/153): libgcc-13.2.1-1.fc40.aarch64.rpm 46 MB/s | 94 kB 00:00 (12/153): libgomp-13.2.1-1.fc40.aarch64.rpm 102 MB/s | 311 kB 00:00 (13/153): libxml2-2.11.5-1.fc40.aarch64.rpm 100 MB/s | 687 kB 00:00 (14/153): libstdc++-13.2.1-1.fc40.aarch64.rpm 86 MB/s | 810 kB 00:00 (15/153): libzstd-1.5.5-4.fc40.aarch64.rpm 43 MB/s | 281 kB 00:00 (16/153): openssl-libs-3.1.1-4.fc40.aarch64.rpm 285 MB/s | 2.0 MB 00:00 (17/153): redhat-rpm-config-270-1.fc40.noarch.r 20 MB/s | 74 kB 00:00 (18/153): zlib-ng-compat-2.1.3-3.fc40.aarch64.r 16 MB/s | 68 kB 00:00 (19/153): zstd-1.5.5-4.fc40.aarch64.rpm 148 MB/s | 446 kB 00:00 (20/153): ansible-srpm-macros-1-11.fc39.noarch. 2.6 MB/s | 21 kB 00:00 (21/153): alternatives-1.25-1.fc39.aarch64.rpm 4.2 MB/s | 38 kB 00:00 (22/153): audit-libs-3.1.2-4.fc40.aarch64.rpm 13 MB/s | 118 kB 00:00 (23/153): authselect-1.4.2-3.fc39.aarch64.rpm 25 MB/s | 144 kB 00:00 (24/153): authselect-libs-1.4.2-3.fc39.aarch64. 38 MB/s | 249 kB 00:00 (25/153): basesystem-11-18.fc39.noarch.rpm 838 kB/s | 7.2 kB 00:00 (26/153): binutils-gold-2.41-5.fc40.aarch64.rpm 21 MB/s | 948 kB 00:00 (27/153): bzip2-1.0.8-16.fc39.aarch64.rpm 15 MB/s | 52 kB 00:00 (28/153): bzip2-libs-1.0.8-16.fc39.aarch64.rpm 12 MB/s | 43 kB 00:00 (29/153): ca-certificates-2023.2.60_v7.0.306-3. 47 MB/s | 837 kB 00:00 (30/153): bash-5.2.15-5.fc39.aarch64.rpm 21 MB/s | 1.8 MB 00:00 (31/153): coreutils-9.4-1.fc40.aarch64.rpm 48 MB/s | 1.2 MB 00:00 (32/153): cpio-2.14-4.fc39.aarch64.rpm 35 MB/s | 277 kB 00:00 (33/153): crypto-policies-20230731-1.git5ed06e0 30 MB/s | 99 kB 00:00 (34/153): coreutils-common-9.4-1.fc40.aarch64.r 35 MB/s | 2.1 MB 00:00 (35/153): cyrus-sasl-lib-2.1.28-11.fc39.aarch64 22 MB/s | 781 kB 00:00 (36/153): debugedit-5.0-10.fc39.aarch64.rpm 23 MB/s | 77 kB 00:00 (37/153): dwz-0.15-3.fc39.aarch64.rpm 26 MB/s | 136 kB 00:00 (38/153): 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-------------------------------------------------------------------------------- Total 82 MB/s | 53 MB 00:00 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xA15B79CC: Userid : "Fedora (40) " Fingerprint: 115D F9AE F857 853E E844 5D0A 0727 707E A15B 79CC From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.aarch64 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-1.fc40.aarch64 1/153 Running scriptlet: libgcc-13.2.1-1.fc40.aarch64 1/153 Installing : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 2/153 Running scriptlet: crypto-policies-20230731-1.git5ed06e0.fc39.noarc 2/153 Installing : tzdata-2023c-3.fc40.noarch 3/153 Installing : fedora-release-identity-basic-40-0.7.noarch 4/153 Installing : fedora-repos-rawhide-40-0.1.noarch 5/153 Installing : fedora-gpg-keys-40-0.1.noarch 6/153 Installing : fedora-repos-40-0.1.noarch 7/153 Installing : fedora-release-common-40-0.7.noarch 8/153 Installing : fedora-release-40-0.7.noarch 9/153 Installing : setup-2.14.4-1.fc39.noarch 10/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.4-1.fc39.noarch 10/153 Installing : filesystem-3.18-6.fc39.aarch64 11/153 Installing : basesystem-11-18.fc39.noarch 12/153 Installing : rust-srpm-macros-24-5.fc40.noarch 13/153 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lz4-libs-1.9.4-4.fc39.aarch64 46/153 Installing : systemd-libs-254.1-2.fc40.aarch64 47/153 Installing : mpfr-4.2.0-3.fc39.aarch64 48/153 Installing : dwz-0.15-3.fc39.aarch64 49/153 Installing : unzip-6.0-62.fc39.aarch64 50/153 Installing : file-libs-5.45-1.fc40.aarch64 51/153 Installing : file-5.45-1.fc40.aarch64 52/153 Installing : alternatives-1.25-1.fc39.aarch64 53/153 Installing : jansson-2.13.1-7.fc39.aarch64 54/153 Installing : libcap-ng-0.8.3-8.fc40.aarch64 55/153 Installing : audit-libs-3.1.2-4.fc40.aarch64 56/153 Installing : pam-libs-1.5.3-2.fc39.aarch64 57/153 Installing : libcom_err-1.47.0-2.fc39.aarch64 58/153 Installing : libsepol-3.5-2.fc39.aarch64 59/153 Installing : libsmartcols-2.39.2-1.fc40.aarch64 60/153 Installing : libunistring-1.1-5.fc40.aarch64 61/153 Installing : libidn2-2.3.4-3.fc39.aarch64 62/153 Installing : lua-libs-5.4.6-3.fc39.aarch64 63/153 Installing : pcre2-10.42-1.fc39.2.aarch64 64/153 Installing : libselinux-3.5-5.fc39.aarch64 65/153 Installing : sed-4.8-14.fc39.aarch64 66/153 Installing : grep-3.11-5.fc40.aarch64 67/153 Installing : findutils-1:4.9.0-6.fc40.aarch64 68/153 Installing : xz-5.4.4-1.fc39.aarch64 69/153 Installing : libmount-2.39.2-1.fc40.aarch64 70/153 Installing : util-linux-core-2.39.2-1.fc40.aarch64 71/153 Installing : libsemanage-3.5-4.fc39.aarch64 72/153 Installing : tar-2:1.35-2.fc40.aarch64 73/153 Installing : libpsl-0.21.2-4.fc39.aarch64 74/153 Installing : zip-3.0-38.fc39.aarch64 75/153 Installing : zstd-1.5.5-4.fc40.aarch64 76/153 Installing : libfdisk-2.39.2-1.fc40.aarch64 77/153 Installing : bzip2-1.0.8-16.fc39.aarch64 78/153 Installing : libxml2-2.11.5-1.fc40.aarch64 79/153 Installing : sqlite-libs-3.43.1-1.fc40.aarch64 80/153 Installing : ed-1.19-4.fc39.aarch64 81/153 Installing : patch-2.7.6-22.fc39.aarch64 82/153 Installing : elfutils-default-yama-scope-0.189-6.fc40.noarch 83/153 Running scriptlet: elfutils-default-yama-scope-0.189-6.fc40.noarch 83/153 Installing : libdb-5.3.28-58.fc40.aarch64 84/153 Installing : libgomp-13.2.1-1.fc40.aarch64 85/153 Installing : cpio-2.14-4.fc39.aarch64 86/153 Installing : diffutils-3.10-3.fc39.aarch64 87/153 Installing : gdbm-libs-1:1.23-4.fc39.aarch64 88/153 Installing : cyrus-sasl-lib-2.1.28-11.fc39.aarch64 89/153 Installing : keyutils-libs-1.6.1-7.fc39.aarch64 90/153 Installing : libbrotli-1.1.0-1.fc40.aarch64 91/153 Installing : libeconf-0.5.2-1.fc40.aarch64 92/153 Installing : shadow-utils-2:4.14.0-1.fc40.aarch64 93/153 Running scriptlet: libutempter-1.2.1-10.fc39.aarch64 94/153 Installing : libutempter-1.2.1-10.fc39.aarch64 94/153 Installing : libffi-3.4.4-4.fc39.aarch64 95/153 Installing : p11-kit-0.25.0-2.fc39.aarch64 96/153 Installing : libnghttp2-1.56.0-1.fc40.aarch64 97/153 Installing : libpkgconf-1.9.5-2.fc39.aarch64 98/153 Installing : pkgconf-1.9.5-2.fc39.aarch64 99/153 Installing : pkgconf-pkg-config-1.9.5-2.fc39.aarch64 100/153 Installing : libsigsegv-2.14-5.fc39.aarch64 101/153 Installing : gawk-5.2.2-2.fc39.aarch64 102/153 Installing : libtasn1-4.19.0-3.fc39.aarch64 103/153 Installing : p11-kit-trust-0.25.0-2.fc39.aarch64 104/153 Running scriptlet: p11-kit-trust-0.25.0-2.fc39.aarch64 104/153 Installing : libverto-0.3.2-6.fc39.aarch64 105/153 Installing : xxhash-libs-0.8.2-1.fc39.aarch64 106/153 Installing : libssh-config-0.10.5-2.fc39.noarch 107/153 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 108/153 Installing : gnat-srpm-macros-6-3.fc39.noarch 109/153 Installing : ghc-srpm-macros-1.6.1-2.fc39.noarch 110/153 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 111/153 Installing : coreutils-common-9.4-1.fc40.aarch64 112/153 Installing : openssl-libs-1:3.1.1-4.fc40.aarch64 113/153 Installing : coreutils-9.4-1.fc40.aarch64 114/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Installing : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Installing : krb5-libs-1.21.2-1.fc40.aarch64 116/153 Installing : libtirpc-1.3.3-1.rc2.fc39.aarch64 117/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.aarch64 118/153 Installing : authselect-libs-1.4.2-3.fc39.aarch64 118/153 Installing : gzip-1.12-6.fc39.aarch64 119/153 Installing : cracklib-2.9.11-2.fc40.aarch64 120/153 Installing : libpwquality-1.4.5-6.fc39.aarch64 121/153 Installing : authselect-1.4.2-3.fc39.aarch64 122/153 Installing : libnsl2-2.0.0-6.fc39.aarch64 123/153 Installing : pam-1.5.3-2.fc39.aarch64 124/153 Installing : libssh-0.10.5-2.fc39.aarch64 125/153 Installing : libarchive-3.7.2-1.fc40.aarch64 126/153 Installing : libevent-2.1.12-9.fc39.aarch64 127/153 Installing : openldap-2.6.6-1.fc39.aarch64 128/153 Installing : libcurl-8.3.0-1.fc40.aarch64 129/153 Installing : elfutils-debuginfod-client-0.189-6.fc40.aarch64 130/153 Installing : elfutils-libs-0.189-6.fc40.aarch64 131/153 Installing : binutils-gold-2.41-5.fc40.aarch64 132/153 Running scriptlet: binutils-gold-2.41-5.fc40.aarch64 132/153 Installing : binutils-2.41-5.fc40.aarch64 133/153 Running scriptlet: binutils-2.41-5.fc40.aarch64 133/153 Installing : elfutils-0.189-6.fc40.aarch64 134/153 Installing : gdb-minimal-13.2-8.fc40.aarch64 135/153 Installing : debugedit-5.0-10.fc39.aarch64 136/153 Installing : curl-8.3.0-1.fc40.aarch64 137/153 Installing : rpm-sequoia-1.5.0-1.fc40.aarch64 138/153 Installing : rpm-libs-4.18.99-1.fc40.aarch64 139/153 Running scriptlet: rpm-4.18.99-1.fc40.aarch64 140/153 Installing : rpm-4.18.99-1.fc40.aarch64 140/153 Installing : efi-srpm-macros-5-9.fc39.noarch 141/153 Installing : lua-srpm-macros-1-9.fc39.noarch 142/153 Installing : rpm-build-libs-4.18.99-1.fc40.aarch64 143/153 Installing : ansible-srpm-macros-1-11.fc39.noarch 144/153 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 145/153 Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 146/153 Installing : go-srpm-macros-3.2.0-7.fc40.noarch 147/153 Installing : python-srpm-macros-3.12-4.fc40.noarch 148/153 Installing : redhat-rpm-config-270-1.fc40.noarch 149/153 Installing : rpm-build-4.18.99-1.fc40.aarch64 150/153 Installing : util-linux-2.39.2-1.fc40.aarch64 151/153 Installing : which-2.21-40.fc39.aarch64 152/153 Installing : info-7.0.3-3.fc39.aarch64 153/153 Running scriptlet: filesystem-3.18-6.fc39.aarch64 153/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.aarch64 153/153 Running scriptlet: rpm-4.18.99-1.fc40.aarch64 153/153 Running scriptlet: info-7.0.3-3.fc39.aarch64 153/153 Verifying : cracklib-2.9.11-2.fc40.aarch64 1/153 Verifying : curl-8.3.0-1.fc40.aarch64 2/153 Verifying : file-5.45-1.fc40.aarch64 3/153 Verifying : file-libs-5.45-1.fc40.aarch64 4/153 Verifying : glibc-2.38.9000-8.fc40.aarch64 5/153 Verifying : glibc-common-2.38.9000-8.fc40.aarch64 6/153 Verifying : glibc-gconv-extra-2.38.9000-8.fc40.aarch64 7/153 Verifying : glibc-minimal-langpack-2.38.9000-8.fc40.aarch64 8/153 Verifying : libcurl-8.3.0-1.fc40.aarch64 9/153 Verifying : libdb-5.3.28-58.fc40.aarch64 10/153 Verifying : libgcc-13.2.1-1.fc40.aarch64 11/153 Verifying : libgomp-13.2.1-1.fc40.aarch64 12/153 Verifying : libstdc++-13.2.1-1.fc40.aarch64 13/153 Verifying : libxml2-2.11.5-1.fc40.aarch64 14/153 Verifying : libzstd-1.5.5-4.fc40.aarch64 15/153 Verifying : openssl-libs-1:3.1.1-4.fc40.aarch64 16/153 Verifying : redhat-rpm-config-270-1.fc40.noarch 17/153 Verifying : zlib-ng-compat-2.1.3-3.fc40.aarch64 18/153 Verifying : zstd-1.5.5-4.fc40.aarch64 19/153 Verifying : alternatives-1.25-1.fc39.aarch64 20/153 Verifying : ansible-srpm-macros-1-11.fc39.noarch 21/153 Verifying : audit-libs-3.1.2-4.fc40.aarch64 22/153 Verifying : authselect-1.4.2-3.fc39.aarch64 23/153 Verifying : authselect-libs-1.4.2-3.fc39.aarch64 24/153 Verifying : basesystem-11-18.fc39.noarch 25/153 Verifying : bash-5.2.15-5.fc39.aarch64 26/153 Verifying : binutils-2.41-5.fc40.aarch64 27/153 Verifying : binutils-gold-2.41-5.fc40.aarch64 28/153 Verifying : bzip2-1.0.8-16.fc39.aarch64 29/153 Verifying : bzip2-libs-1.0.8-16.fc39.aarch64 30/153 Verifying : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 31/153 Verifying : coreutils-9.4-1.fc40.aarch64 32/153 Verifying : coreutils-common-9.4-1.fc40.aarch64 33/153 Verifying : cpio-2.14-4.fc39.aarch64 34/153 Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 35/153 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.aarch64 36/153 Verifying : debugedit-5.0-10.fc39.aarch64 37/153 Verifying : diffutils-3.10-3.fc39.aarch64 38/153 Verifying : dwz-0.15-3.fc39.aarch64 39/153 Verifying : ed-1.19-4.fc39.aarch64 40/153 Verifying : efi-srpm-macros-5-9.fc39.noarch 41/153 Verifying : elfutils-0.189-6.fc40.aarch64 42/153 Verifying : elfutils-debuginfod-client-0.189-6.fc40.aarch64 43/153 Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 44/153 Verifying : elfutils-libelf-0.189-6.fc40.aarch64 45/153 Verifying : elfutils-libs-0.189-6.fc40.aarch64 46/153 Verifying : fedora-gpg-keys-40-0.1.noarch 47/153 Verifying : fedora-release-40-0.7.noarch 48/153 Verifying : fedora-release-common-40-0.7.noarch 49/153 Verifying : fedora-release-identity-basic-40-0.7.noarch 50/153 Verifying : fedora-repos-40-0.1.noarch 51/153 Verifying : fedora-repos-rawhide-40-0.1.noarch 52/153 Verifying : filesystem-3.18-6.fc39.aarch64 53/153 Verifying : findutils-1:4.9.0-6.fc40.aarch64 54/153 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 55/153 Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 56/153 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 57/153 Verifying : gawk-5.2.2-2.fc39.aarch64 58/153 Verifying : gdb-minimal-13.2-8.fc40.aarch64 59/153 Verifying : gdbm-libs-1:1.23-4.fc39.aarch64 60/153 Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 61/153 Verifying : gmp-1:6.2.1-5.fc39.aarch64 62/153 Verifying : gnat-srpm-macros-6-3.fc39.noarch 63/153 Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 64/153 Verifying : grep-3.11-5.fc40.aarch64 65/153 Verifying : gzip-1.12-6.fc39.aarch64 66/153 Verifying : info-7.0.3-3.fc39.aarch64 67/153 Verifying : jansson-2.13.1-7.fc39.aarch64 68/153 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 69/153 Verifying : keyutils-libs-1.6.1-7.fc39.aarch64 70/153 Verifying : krb5-libs-1.21.2-1.fc40.aarch64 71/153 Verifying : libacl-2.3.1-9.fc40.aarch64 72/153 Verifying : libarchive-3.7.2-1.fc40.aarch64 73/153 Verifying : libattr-2.5.1-9.fc40.aarch64 74/153 Verifying : libblkid-2.39.2-1.fc40.aarch64 75/153 Verifying : libbrotli-1.1.0-1.fc40.aarch64 76/153 Verifying : libcap-2.48-7.fc39.aarch64 77/153 Verifying : libcap-ng-0.8.3-8.fc40.aarch64 78/153 Verifying : libcom_err-1.47.0-2.fc39.aarch64 79/153 Verifying : libeconf-0.5.2-1.fc40.aarch64 80/153 Verifying : libevent-2.1.12-9.fc39.aarch64 81/153 Verifying : libfdisk-2.39.2-1.fc40.aarch64 82/153 Verifying : libffi-3.4.4-4.fc39.aarch64 83/153 Verifying : libidn2-2.3.4-3.fc39.aarch64 84/153 Verifying : libmount-2.39.2-1.fc40.aarch64 85/153 Verifying : libnghttp2-1.56.0-1.fc40.aarch64 86/153 Verifying : libnsl2-2.0.0-6.fc39.aarch64 87/153 Verifying : libpkgconf-1.9.5-2.fc39.aarch64 88/153 Verifying : libpsl-0.21.2-4.fc39.aarch64 89/153 Verifying : libpwquality-1.4.5-6.fc39.aarch64 90/153 Verifying : libselinux-3.5-5.fc39.aarch64 91/153 Verifying : libsemanage-3.5-4.fc39.aarch64 92/153 Verifying : libsepol-3.5-2.fc39.aarch64 93/153 Verifying : libsigsegv-2.14-5.fc39.aarch64 94/153 Verifying : libsmartcols-2.39.2-1.fc40.aarch64 95/153 Verifying : libssh-0.10.5-2.fc39.aarch64 96/153 Verifying : libssh-config-0.10.5-2.fc39.noarch 97/153 Verifying : libtasn1-4.19.0-3.fc39.aarch64 98/153 Verifying : libtirpc-1.3.3-1.rc2.fc39.aarch64 99/153 Verifying : libunistring-1.1-5.fc40.aarch64 100/153 Verifying : libutempter-1.2.1-10.fc39.aarch64 101/153 Verifying : libuuid-2.39.2-1.fc40.aarch64 102/153 Verifying : libverto-0.3.2-6.fc39.aarch64 103/153 Verifying : libxcrypt-4.4.36-2.fc39.aarch64 104/153 Verifying : lua-libs-5.4.6-3.fc39.aarch64 105/153 Verifying : lua-srpm-macros-1-9.fc39.noarch 106/153 Verifying : lz4-libs-1.9.4-4.fc39.aarch64 107/153 Verifying : mpfr-4.2.0-3.fc39.aarch64 108/153 Verifying : ncurses-base-6.4-7.20230520.fc40.noarch 109/153 Verifying : ncurses-libs-6.4-7.20230520.fc40.aarch64 110/153 Verifying : ocaml-srpm-macros-8-2.fc39.noarch 111/153 Verifying : openblas-srpm-macros-2-14.fc39.noarch 112/153 Verifying : openldap-2.6.6-1.fc39.aarch64 113/153 Verifying : p11-kit-0.25.0-2.fc39.aarch64 114/153 Verifying : p11-kit-trust-0.25.0-2.fc39.aarch64 115/153 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 116/153 Verifying : pam-1.5.3-2.fc39.aarch64 117/153 Verifying : pam-libs-1.5.3-2.fc39.aarch64 118/153 Verifying : patch-2.7.6-22.fc39.aarch64 119/153 Verifying : pcre2-10.42-1.fc39.2.aarch64 120/153 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 121/153 Verifying : perl-srpm-macros-1-51.fc39.noarch 122/153 Verifying : pkgconf-1.9.5-2.fc39.aarch64 123/153 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 124/153 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.aarch64 125/153 Verifying : popt-1.19-3.fc39.aarch64 126/153 Verifying : publicsuffix-list-dafsa-20230812-1.fc40.noarch 127/153 Verifying : pyproject-srpm-macros-1.9.0-2.fc39.noarch 128/153 Verifying : python-srpm-macros-3.12-4.fc40.noarch 129/153 Verifying : qt5-srpm-macros-5.15.10-2.fc39.noarch 130/153 Verifying : qt6-srpm-macros-6.5.2-2.fc39.noarch 131/153 Verifying : readline-8.2-4.fc39.aarch64 132/153 Verifying : rpm-4.18.99-1.fc40.aarch64 133/153 Verifying : rpm-build-4.18.99-1.fc40.aarch64 134/153 Verifying : rpm-build-libs-4.18.99-1.fc40.aarch64 135/153 Verifying : rpm-libs-4.18.99-1.fc40.aarch64 136/153 Verifying : rpm-sequoia-1.5.0-1.fc40.aarch64 137/153 Verifying : rust-srpm-macros-24-5.fc40.noarch 138/153 Verifying : sed-4.8-14.fc39.aarch64 139/153 Verifying : setup-2.14.4-1.fc39.noarch 140/153 Verifying : shadow-utils-2:4.14.0-1.fc40.aarch64 141/153 Verifying : sqlite-libs-3.43.1-1.fc40.aarch64 142/153 Verifying : systemd-libs-254.1-2.fc40.aarch64 143/153 Verifying : tar-2:1.35-2.fc40.aarch64 144/153 Verifying : tzdata-2023c-3.fc40.noarch 145/153 Verifying : unzip-6.0-62.fc39.aarch64 146/153 Verifying : util-linux-2.39.2-1.fc40.aarch64 147/153 Verifying : util-linux-core-2.39.2-1.fc40.aarch64 148/153 Verifying : which-2.21-40.fc39.aarch64 149/153 Verifying : xxhash-libs-0.8.2-1.fc39.aarch64 150/153 Verifying : xz-5.4.4-1.fc39.aarch64 151/153 Verifying : xz-libs-5.4.4-1.fc39.aarch64 152/153 Verifying : zip-3.0-38.fc39.aarch64 153/153 Installed: alternatives-1.25-1.fc39.aarch64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.aarch64 authselect-1.4.2-3.fc39.aarch64 authselect-libs-1.4.2-3.fc39.aarch64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.aarch64 binutils-2.41-5.fc40.aarch64 binutils-gold-2.41-5.fc40.aarch64 bzip2-1.0.8-16.fc39.aarch64 bzip2-libs-1.0.8-16.fc39.aarch64 ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.aarch64 coreutils-common-9.4-1.fc40.aarch64 cpio-2.14-4.fc39.aarch64 cracklib-2.9.11-2.fc40.aarch64 crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.aarch64 cyrus-sasl-lib-2.1.28-11.fc39.aarch64 debugedit-5.0-10.fc39.aarch64 diffutils-3.10-3.fc39.aarch64 dwz-0.15-3.fc39.aarch64 ed-1.19-4.fc39.aarch64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.aarch64 elfutils-debuginfod-client-0.189-6.fc40.aarch64 elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.aarch64 elfutils-libs-0.189-6.fc40.aarch64 fedora-gpg-keys-40-0.1.noarch fedora-release-40-0.7.noarch fedora-release-common-40-0.7.noarch fedora-release-identity-basic-40-0.7.noarch fedora-repos-40-0.1.noarch fedora-repos-rawhide-40-0.1.noarch file-5.45-1.fc40.aarch64 file-libs-5.45-1.fc40.aarch64 filesystem-3.18-6.fc39.aarch64 findutils-1:4.9.0-6.fc40.aarch64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.aarch64 gdb-minimal-13.2-8.fc40.aarch64 gdbm-libs-1:1.23-4.fc39.aarch64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.aarch64 glibc-common-2.38.9000-8.fc40.aarch64 glibc-gconv-extra-2.38.9000-8.fc40.aarch64 glibc-minimal-langpack-2.38.9000-8.fc40.aarch64 gmp-1:6.2.1-5.fc39.aarch64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-7.fc40.noarch grep-3.11-5.fc40.aarch64 gzip-1.12-6.fc39.aarch64 info-7.0.3-3.fc39.aarch64 jansson-2.13.1-7.fc39.aarch64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.aarch64 krb5-libs-1.21.2-1.fc40.aarch64 libacl-2.3.1-9.fc40.aarch64 libarchive-3.7.2-1.fc40.aarch64 libattr-2.5.1-9.fc40.aarch64 libblkid-2.39.2-1.fc40.aarch64 libbrotli-1.1.0-1.fc40.aarch64 libcap-2.48-7.fc39.aarch64 libcap-ng-0.8.3-8.fc40.aarch64 libcom_err-1.47.0-2.fc39.aarch64 libcurl-8.3.0-1.fc40.aarch64 libdb-5.3.28-58.fc40.aarch64 libeconf-0.5.2-1.fc40.aarch64 libevent-2.1.12-9.fc39.aarch64 libfdisk-2.39.2-1.fc40.aarch64 libffi-3.4.4-4.fc39.aarch64 libgcc-13.2.1-1.fc40.aarch64 libgomp-13.2.1-1.fc40.aarch64 libidn2-2.3.4-3.fc39.aarch64 libmount-2.39.2-1.fc40.aarch64 libnghttp2-1.56.0-1.fc40.aarch64 libnsl2-2.0.0-6.fc39.aarch64 libpkgconf-1.9.5-2.fc39.aarch64 libpsl-0.21.2-4.fc39.aarch64 libpwquality-1.4.5-6.fc39.aarch64 libselinux-3.5-5.fc39.aarch64 libsemanage-3.5-4.fc39.aarch64 libsepol-3.5-2.fc39.aarch64 libsigsegv-2.14-5.fc39.aarch64 libsmartcols-2.39.2-1.fc40.aarch64 libssh-0.10.5-2.fc39.aarch64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc40.aarch64 libtasn1-4.19.0-3.fc39.aarch64 libtirpc-1.3.3-1.rc2.fc39.aarch64 libunistring-1.1-5.fc40.aarch64 libutempter-1.2.1-10.fc39.aarch64 libuuid-2.39.2-1.fc40.aarch64 libverto-0.3.2-6.fc39.aarch64 libxcrypt-4.4.36-2.fc39.aarch64 libxml2-2.11.5-1.fc40.aarch64 libzstd-1.5.5-4.fc40.aarch64 lua-libs-5.4.6-3.fc39.aarch64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.aarch64 mpfr-4.2.0-3.fc39.aarch64 ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.aarch64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.aarch64 openssl-libs-1:3.1.1-4.fc40.aarch64 p11-kit-0.25.0-2.fc39.aarch64 p11-kit-trust-0.25.0-2.fc39.aarch64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.aarch64 pam-libs-1.5.3-2.fc39.aarch64 patch-2.7.6-22.fc39.aarch64 pcre2-10.42-1.fc39.2.aarch64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.aarch64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.aarch64 popt-1.19-3.fc39.aarch64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.10-2.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch readline-8.2-4.fc39.aarch64 redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.aarch64 rpm-build-4.18.99-1.fc40.aarch64 rpm-build-libs-4.18.99-1.fc40.aarch64 rpm-libs-4.18.99-1.fc40.aarch64 rpm-sequoia-1.5.0-1.fc40.aarch64 rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.aarch64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-1.fc40.aarch64 sqlite-libs-3.43.1-1.fc40.aarch64 systemd-libs-254.1-2.fc40.aarch64 tar-2:1.35-2.fc40.aarch64 tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.aarch64 util-linux-2.39.2-1.fc40.aarch64 util-linux-core-2.39.2-1.fc40.aarch64 which-2.21-40.fc39.aarch64 xxhash-libs-0.8.2-1.fc39.aarch64 xz-5.4.4-1.fc39.aarch64 xz-libs-5.4.4-1.fc39.aarch64 zip-3.0-38.fc39.aarch64 zlib-ng-compat-2.1.3-3.fc40.aarch64 zstd-1.5.5-4.fc40.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.aarch64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.aarch64 authselect-1.4.2-3.fc39.aarch64 authselect-libs-1.4.2-3.fc39.aarch64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.aarch64 binutils-2.41-5.fc40.aarch64 binutils-gold-2.41-5.fc40.aarch64 bzip2-1.0.8-16.fc39.aarch64 bzip2-libs-1.0.8-16.fc39.aarch64 ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.aarch64 coreutils-common-9.4-1.fc40.aarch64 cpio-2.14-4.fc39.aarch64 cracklib-2.9.11-2.fc40.aarch64 crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.aarch64 cyrus-sasl-lib-2.1.28-11.fc39.aarch64 debugedit-5.0-10.fc39.aarch64 diffutils-3.10-3.fc39.aarch64 dwz-0.15-3.fc39.aarch64 ed-1.19-4.fc39.aarch64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.aarch64 elfutils-debuginfod-client-0.189-6.fc40.aarch64 elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.aarch64 elfutils-libs-0.189-6.fc40.aarch64 fedora-gpg-keys-40-0.1.noarch fedora-release-40-0.7.noarch fedora-release-common-40-0.7.noarch fedora-release-identity-basic-40-0.7.noarch fedora-repos-40-0.1.noarch fedora-repos-rawhide-40-0.1.noarch file-5.45-1.fc40.aarch64 file-libs-5.45-1.fc40.aarch64 filesystem-3.18-6.fc39.aarch64 findutils-4.9.0-6.fc40.aarch64 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.aarch64 gdb-minimal-13.2-8.fc40.aarch64 gdbm-libs-1.23-4.fc39.aarch64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.aarch64 glibc-common-2.38.9000-8.fc40.aarch64 glibc-gconv-extra-2.38.9000-8.fc40.aarch64 glibc-minimal-langpack-2.38.9000-8.fc40.aarch64 gmp-6.2.1-5.fc39.aarch64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-7.fc40.noarch gpg-pubkey-18b8e74c-62f2920f gpg-pubkey-a15b79cc-63d04c2c grep-3.11-5.fc40.aarch64 gzip-1.12-6.fc39.aarch64 info-7.0.3-3.fc39.aarch64 jansson-2.13.1-7.fc39.aarch64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.aarch64 krb5-libs-1.21.2-1.fc40.aarch64 libacl-2.3.1-9.fc40.aarch64 libarchive-3.7.2-1.fc40.aarch64 libattr-2.5.1-9.fc40.aarch64 libblkid-2.39.2-1.fc40.aarch64 libbrotli-1.1.0-1.fc40.aarch64 libcap-2.48-7.fc39.aarch64 libcap-ng-0.8.3-8.fc40.aarch64 libcom_err-1.47.0-2.fc39.aarch64 libcurl-8.3.0-1.fc40.aarch64 libdb-5.3.28-58.fc40.aarch64 libeconf-0.5.2-1.fc40.aarch64 libevent-2.1.12-9.fc39.aarch64 libfdisk-2.39.2-1.fc40.aarch64 libffi-3.4.4-4.fc39.aarch64 libgcc-13.2.1-1.fc40.aarch64 libgomp-13.2.1-1.fc40.aarch64 libidn2-2.3.4-3.fc39.aarch64 libmount-2.39.2-1.fc40.aarch64 libnghttp2-1.56.0-1.fc40.aarch64 libnsl2-2.0.0-6.fc39.aarch64 libpkgconf-1.9.5-2.fc39.aarch64 libpsl-0.21.2-4.fc39.aarch64 libpwquality-1.4.5-6.fc39.aarch64 libselinux-3.5-5.fc39.aarch64 libsemanage-3.5-4.fc39.aarch64 libsepol-3.5-2.fc39.aarch64 libsigsegv-2.14-5.fc39.aarch64 libsmartcols-2.39.2-1.fc40.aarch64 libssh-0.10.5-2.fc39.aarch64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc40.aarch64 libtasn1-4.19.0-3.fc39.aarch64 libtirpc-1.3.3-1.rc2.fc39.aarch64 libunistring-1.1-5.fc40.aarch64 libutempter-1.2.1-10.fc39.aarch64 libuuid-2.39.2-1.fc40.aarch64 libverto-0.3.2-6.fc39.aarch64 libxcrypt-4.4.36-2.fc39.aarch64 libxml2-2.11.5-1.fc40.aarch64 libzstd-1.5.5-4.fc40.aarch64 lua-libs-5.4.6-3.fc39.aarch64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.aarch64 mpfr-4.2.0-3.fc39.aarch64 ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.aarch64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.aarch64 openssl-libs-3.1.1-4.fc40.aarch64 p11-kit-0.25.0-2.fc39.aarch64 p11-kit-trust-0.25.0-2.fc39.aarch64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.aarch64 pam-libs-1.5.3-2.fc39.aarch64 patch-2.7.6-22.fc39.aarch64 pcre2-10.42-1.fc39.2.aarch64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.aarch64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.aarch64 popt-1.19-3.fc39.aarch64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.10-2.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch readline-8.2-4.fc39.aarch64 redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.aarch64 rpm-build-4.18.99-1.fc40.aarch64 rpm-build-libs-4.18.99-1.fc40.aarch64 rpm-libs-4.18.99-1.fc40.aarch64 rpm-sequoia-1.5.0-1.fc40.aarch64 rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.aarch64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-1.fc40.aarch64 sqlite-libs-3.43.1-1.fc40.aarch64 systemd-libs-254.1-2.fc40.aarch64 tar-1.35-2.fc40.aarch64 tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.aarch64 util-linux-2.39.2-1.fc40.aarch64 util-linux-core-2.39.2-1.fc40.aarch64 which-2.21-40.fc39.aarch64 xxhash-libs-0.8.2-1.fc39.aarch64 xz-5.4.4-1.fc39.aarch64 xz-libs-5.4.4-1.fc39.aarch64 zip-3.0-38.fc39.aarch64 zlib-ng-compat-2.1.3-3.fc40.aarch64 zstd-1.5.5-4.fc40.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1693872000 Wrote: /builddir/build/SRPMS/python-pysam-0.21.0-2.fc40.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-q0omb0sp/python-pysam/python-pysam.spec) Config(child) 1 minutes 0 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-0.21.0-2.fc40.src.rpm) Config(fedora-rawhide-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1694965618.485673/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1694965618.485673/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-aarch64-1694965618.485673/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 Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.18.99-1.fc40.aarch64 rpm-sequoia-1.5.0-1.fc40.aarch64 python3-dnf-4.16.2-4.fc40.noarch python3-dnf-plugins-core-4.4.2-1.fc39.noarch yum-4.16.2-4.fc40.noarch Start: build phase for python-pysam-0.21.0-2.fc40.src.rpm Start: build setup for python-pysam-0.21.0-2.fc40.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1693872000 Wrote: /builddir/build/SRPMS/python-pysam-0.21.0-2.fc40.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 53 kB/s | 1.5 kB 00:00 fedora 29 kB/s | 7.3 kB 00:00 Dependencies resolved. ========================================================================================== Package Arch Version Repo Size ========================================================================================== Installing: bzip2-devel aarch64 1.0.8-16.fc39 fedora 214 k gcc aarch64 13.2.1-1.fc40 copr_base 31 M python3-cython aarch64 3.0.2-1.fc40 fedora 3.7 M python3-devel aarch64 3.12.0~rc2-1.fc40 fedora 311 k python3-setuptools noarch 67.7.2-7.fc40 fedora 1.5 M python3-sphinx noarch 1:7.1.2-1.fc40 fedora 2.6 M xz-devel aarch64 5.4.4-1.fc39 fedora 66 k zlib-ng-compat-devel aarch64 2.1.3-3.fc40 copr_base 34 k Installing dependencies: annobin-docs noarch 12.26-1.fc40 fedora 94 k annobin-plugin-gcc aarch64 12.26-1.fc40 fedora 958 k cpp aarch64 13.2.1-1.fc40 copr_base 9.7 M expat aarch64 2.5.0-3.fc39 fedora 108 k gc aarch64 8.2.2-4.fc39 fedora 110 k gcc-plugin-annobin aarch64 13.2.1-1.fc40 copr_base 47 k glibc-devel aarch64 2.38.9000-8.fc40 copr_base 503 k guile22 aarch64 2.2.7-9.fc39 fedora 6.5 M kernel-headers aarch64 6.6.0-0.rc1.git0.1.fc40 fedora 1.5 M libasan aarch64 13.2.1-1.fc40 copr_base 455 k libatomic aarch64 13.2.1-1.fc40 copr_base 36 k libb2 aarch64 0.98.1-9.fc39 fedora 24 k libmpc aarch64 1.3.1-3.fc39 fedora 72 k libtool-ltdl aarch64 2.4.7-8.fc40 fedora 36 k libubsan aarch64 13.2.1-1.fc40 copr_base 204 k libxcrypt-devel aarch64 4.4.36-2.fc39 fedora 30 k make aarch64 1:4.4.1-2.fc39 fedora 585 k mpdecimal aarch64 2.5.1-7.fc39 fedora 90 k pyproject-rpm-macros noarch 1.9.0-2.fc39 fedora 41 k python-pip-wheel noarch 23.2.1-1.fc39 fedora 1.5 M python-rpm-macros noarch 3.12-4.fc40 fedora 19 k python3 aarch64 3.12.0~rc2-1.fc40 fedora 26 k python3-babel noarch 2.12.1-4.fc39~bootstrap fedora 6.9 M python3-charset-normalizer noarch 3.2.0-2.fc39 fedora 105 k python3-docutils noarch 0.20.1-1.fc40 fedora 1.0 M python3-idna noarch 3.4-5.fc40 fedora 109 k python3-imagesize noarch 1.4.1-5.fc40 fedora 22 k python3-jinja2 noarch 3.1.2-6.fc40 fedora 505 k python3-libs aarch64 3.12.0~rc2-1.fc40 fedora 9.1 M python3-markupsafe aarch64 2.1.3-2.fc39 fedora 30 k python3-packaging noarch 23.1-5.fc40 fedora 115 k python3-pygments noarch 2.16.1-1.fc40 fedora 2.4 M python3-pysocks noarch 1.7.1-20.fc39 fedora 39 k python3-requests noarch 2.28.2-6.fc40 fedora 151 k python3-rpm-generators noarch 14-7.fc39 fedora 30 k python3-rpm-macros noarch 3.12-4.fc40 fedora 14 k python3-snowballstemmer noarch 2.2.0-7.fc39 fedora 257 k python3-sphinx-theme-alabaster noarch 0.7.12-19.fc39 fedora 29 k python3-sphinxcontrib-applehelp noarch 1.0.6-1.fc40 fedora 45 k python3-sphinxcontrib-devhelp noarch 1.0.2-14.fc39 fedora 41 k python3-sphinxcontrib-htmlhelp noarch 2.0.3-1.fc40 fedora 54 k python3-sphinxcontrib-jsmath noarch 1.0.1-22.fc39 fedora 17 k python3-sphinxcontrib-qthelp noarch 1.0.3-15.fc39 fedora 47 k python3-sphinxcontrib-serializinghtml noarch 1.1.5-10.fc39 fedora 47 k python3-urllib3 noarch 1.26.16-3.fc40 fedora 273 k python3-urllib3+socks noarch 1.26.16-3.fc40 fedora 9.9 k Transaction Summary ========================================================================================== Install 54 Packages Total download size: 84 M Installed size: 319 M Downloading Packages: (1/54): gcc-plugin-annobin-13.2.1-1.fc40.aarch6 2.7 MB/s | 47 kB 00:00 (2/54): glibc-devel-2.38.9000-8.fc40.aarch64.rp 22 MB/s | 503 kB 00:00 (3/54): libasan-13.2.1-1.fc40.aarch64.rpm 126 MB/s | 455 kB 00:00 (4/54): libatomic-13.2.1-1.fc40.aarch64.rpm 22 MB/s | 36 kB 00:00 (5/54): libubsan-13.2.1-1.fc40.aarch64.rpm 19 MB/s | 204 kB 00:00 (6/54): zlib-ng-compat-devel-2.1.3-3.fc40.aarch 3.6 MB/s | 34 kB 00:00 (7/54): cpp-13.2.1-1.fc40.aarch64.rpm 87 MB/s | 9.7 MB 00:00 (8/54): annobin-docs-12.26-1.fc40.noarch.rpm 2.4 MB/s | 94 kB 00:00 (9/54): gcc-13.2.1-1.fc40.aarch64.rpm 218 MB/s | 31 MB 00:00 (10/54): bzip2-devel-1.0.8-16.fc39.aarch64.rpm 6.8 MB/s | 214 kB 00:00 (11/54): annobin-plugin-gcc-12.26-1.fc40.aarch6 27 MB/s | 958 kB 00:00 (12/54): expat-2.5.0-3.fc39.aarch64.rpm 21 MB/s | 108 kB 00:00 (13/54): gc-8.2.2-4.fc39.aarch64.rpm 29 MB/s | 110 kB 00:00 (14/54): libb2-0.98.1-9.fc39.aarch64.rpm 5.1 MB/s | 24 kB 00:00 (15/54): libmpc-1.3.1-3.fc39.aarch64.rpm 21 MB/s | 72 kB 00:00 (16/54): libtool-ltdl-2.4.7-8.fc40.aarch64.rpm 1.6 MB/s | 36 kB 00:00 (17/54): libxcrypt-devel-4.4.36-2.fc39.aarch64. 9.0 MB/s | 30 kB 00:00 (18/54): kernel-headers-6.6.0-0.rc1.git0.1.fc40 39 MB/s | 1.5 MB 00:00 (19/54): mpdecimal-2.5.1-7.fc39.aarch64.rpm 14 MB/s | 90 kB 00:00 (20/54): pyproject-rpm-macros-1.9.0-2.fc39.noar 19 MB/s | 41 kB 00:00 (21/54): make-4.4.1-2.fc39.aarch64.rpm 15 MB/s | 585 kB 00:00 (22/54): python-rpm-macros-3.12-4.fc40.noarch.r 9.8 MB/s | 19 kB 00:00 (23/54): python3-3.12.0~rc2-1.fc40.aarch64.rpm 7.8 MB/s | 26 kB 00:00 (24/54): python-pip-wheel-23.2.1-1.fc39.noarch. 20 MB/s | 1.5 MB 00:00 (25/54): python3-charset-normalizer-3.2.0-2.fc3 14 MB/s | 105 kB 00:00 (26/54): python3-cython-3.0.2-1.fc40.aarch64.rp 167 MB/s | 3.7 MB 00:00 (27/54): python3-devel-3.12.0~rc2-1.fc40.aarch6 114 MB/s | 311 kB 00:00 (28/54): python3-docutils-0.20.1-1.fc40.noarch. 27 MB/s | 1.0 MB 00:00 (29/54): python3-idna-3.4-5.fc40.noarch.rpm 21 MB/s | 109 kB 00:00 (30/54): python3-imagesize-1.4.1-5.fc40.noarch. 6.2 MB/s | 22 kB 00:00 (31/54): guile22-2.2.7-9.fc39.aarch64.rpm 29 MB/s | 6.5 MB 00:00 (32/54): python3-babel-2.12.1-4.fc39~bootstrap. 46 MB/s | 6.9 MB 00:00 (33/54): python3-jinja2-3.1.2-6.fc40.noarch.rpm 18 MB/s | 505 kB 00:00 (34/54): python3-markupsafe-2.1.3-2.fc39.aarch6 9.0 MB/s | 30 kB 00:00 (35/54): python3-packaging-23.1-5.fc40.noarch.r 45 MB/s | 115 kB 00:00 (36/54): python3-pysocks-1.7.1-20.fc39.noarch.r 7.0 MB/s | 39 kB 00:00 (37/54): python3-requests-2.28.2-6.fc40.noarch. 12 MB/s | 151 kB 00:00 (38/54): python3-pygments-2.16.1-1.fc40.noarch. 97 MB/s | 2.4 MB 00:00 (39/54): python3-rpm-generators-14-7.fc39.noarc 6.9 MB/s | 30 kB 00:00 (40/54): python3-rpm-macros-3.12-4.fc40.noarch. 9.0 MB/s | 14 kB 00:00 (41/54): python3-snowballstemmer-2.2.0-7.fc39.n 36 MB/s | 257 kB 00:00 (42/54): python3-setuptools-67.7.2-7.fc40.noarc 37 MB/s | 1.5 MB 00:00 (43/54): python3-sphinx-7.1.2-1.fc40.noarch.rpm 66 MB/s | 2.6 MB 00:00 (44/54): python3-sphinx-theme-alabaster-0.7.12- 3.6 MB/s | 29 kB 00:00 (45/54): python3-sphinxcontrib-applehelp-1.0.6- 13 MB/s | 45 kB 00:00 (46/54): python3-sphinxcontrib-devhelp-1.0.2-14 12 MB/s | 41 kB 00:00 (47/54): python3-sphinxcontrib-jsmath-1.0.1-22. 6.3 MB/s | 17 kB 00:00 (48/54): python3-sphinxcontrib-htmlhelp-2.0.3-1 11 MB/s | 54 kB 00:00 (49/54): python3-sphinxcontrib-qthelp-1.0.3-15. 9.8 MB/s | 47 kB 00:00 (50/54): python3-sphinxcontrib-serializinghtml- 13 MB/s | 47 kB 00:00 (51/54): python3-urllib3+socks-1.26.16-3.fc40.n 3.1 MB/s | 9.9 kB 00:00 (52/54): xz-devel-5.4.4-1.fc39.aarch64.rpm 25 MB/s | 66 kB 00:00 (53/54): python3-urllib3-1.26.16-3.fc40.noarch. 31 MB/s | 273 kB 00:00 (54/54): python3-libs-3.12.0~rc2-1.fc40.aarch64 48 MB/s | 9.1 MB 00:00 -------------------------------------------------------------------------------- Total 128 MB/s | 84 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.12-4.fc40.noarch 1/54 Installing : python3-rpm-macros-3.12-4.fc40.noarch 2/54 Installing : libmpc-1.3.1-3.fc39.aarch64 3/54 Installing : cpp-13.2.1-1.fc40.aarch64 4/54 Installing : pyproject-rpm-macros-1.9.0-2.fc39.noarch 5/54 Installing : python-pip-wheel-23.2.1-1.fc39.noarch 6/54 Installing : mpdecimal-2.5.1-7.fc39.aarch64 7/54 Installing : libtool-ltdl-2.4.7-8.fc40.aarch64 8/54 Installing : libb2-0.98.1-9.fc39.aarch64 9/54 Installing : kernel-headers-6.6.0-0.rc1.git0.1.fc40.aarch64 10/54 Installing : libxcrypt-devel-4.4.36-2.fc39.aarch64 11/54 Installing : glibc-devel-2.38.9000-8.fc40.aarch64 12/54 Installing : gc-8.2.2-4.fc39.aarch64 13/54 Installing : guile22-2.2.7-9.fc39.aarch64 14/54 Installing : make-1:4.4.1-2.fc39.aarch64 15/54 Installing : expat-2.5.0-3.fc39.aarch64 16/54 Installing : python3-3.12.0~rc2-1.fc40.aarch64 17/54 Installing : python3-libs-3.12.0~rc2-1.fc40.aarch64 18/54 Installing : python3-idna-3.4-5.fc40.noarch 19/54 Installing : python3-packaging-23.1-5.fc40.noarch 20/54 Installing : python3-rpm-generators-14-7.fc39.noarch 21/54 Installing : python3-babel-2.12.1-4.fc39~bootstrap.noarch 22/54 Installing : python3-charset-normalizer-3.2.0-2.fc39.noarch 23/54 Installing : python3-docutils-0.20.1-1.fc40.noarch 24/54 Installing : python3-imagesize-1.4.1-5.fc40.noarch 25/54 Installing : python3-markupsafe-2.1.3-2.fc39.aarch64 26/54 Installing : python3-jinja2-3.1.2-6.fc40.noarch 27/54 Installing : python3-pygments-2.16.1-1.fc40.noarch 28/54 Installing : python3-pysocks-1.7.1-20.fc39.noarch 29/54 Installing : python3-urllib3+socks-1.26.16-3.fc40.noarch 30/54 Installing : python3-urllib3-1.26.16-3.fc40.noarch 31/54 Installing : python3-requests-2.28.2-6.fc40.noarch 32/54 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 33/54 Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 34/54 Installing : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 35/54 Installing : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 36/54 Installing : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 37/54 Installing : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 38/54 Installing : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 39/54 Installing : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 40/54 Installing : python3-sphinx-1:7.1.2-1.fc40.noarch 41/54 Installing : annobin-docs-12.26-1.fc40.noarch 42/54 Installing : libubsan-13.2.1-1.fc40.aarch64 43/54 Installing : libatomic-13.2.1-1.fc40.aarch64 44/54 Installing : libasan-13.2.1-1.fc40.aarch64 45/54 Installing : gcc-13.2.1-1.fc40.aarch64 46/54 Running scriptlet: gcc-13.2.1-1.fc40.aarch64 46/54 Installing : gcc-plugin-annobin-13.2.1-1.fc40.aarch64 47/54 Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc40.aarch64 47/54 Installing : annobin-plugin-gcc-12.26-1.fc40.aarch64 48/54 Running scriptlet: annobin-plugin-gcc-12.26-1.fc40.aarch64 48/54 Installing : python3-devel-3.12.0~rc2-1.fc40.aarch64 49/54 Installing : python3-cython-3.0.2-1.fc40.aarch64 50/54 Installing : python3-setuptools-67.7.2-7.fc40.noarch 51/54 Installing : xz-devel-5.4.4-1.fc39.aarch64 52/54 Installing : bzip2-devel-1.0.8-16.fc39.aarch64 53/54 Installing : zlib-ng-compat-devel-2.1.3-3.fc40.aarch64 54/54 Running scriptlet: zlib-ng-compat-devel-2.1.3-3.fc40.aarch64 54/54 Verifying : cpp-13.2.1-1.fc40.aarch64 1/54 Verifying : gcc-13.2.1-1.fc40.aarch64 2/54 Verifying : gcc-plugin-annobin-13.2.1-1.fc40.aarch64 3/54 Verifying : glibc-devel-2.38.9000-8.fc40.aarch64 4/54 Verifying : libasan-13.2.1-1.fc40.aarch64 5/54 Verifying : libatomic-13.2.1-1.fc40.aarch64 6/54 Verifying : libubsan-13.2.1-1.fc40.aarch64 7/54 Verifying : zlib-ng-compat-devel-2.1.3-3.fc40.aarch64 8/54 Verifying : annobin-docs-12.26-1.fc40.noarch 9/54 Verifying : annobin-plugin-gcc-12.26-1.fc40.aarch64 10/54 Verifying : bzip2-devel-1.0.8-16.fc39.aarch64 11/54 Verifying : expat-2.5.0-3.fc39.aarch64 12/54 Verifying : gc-8.2.2-4.fc39.aarch64 13/54 Verifying : guile22-2.2.7-9.fc39.aarch64 14/54 Verifying : kernel-headers-6.6.0-0.rc1.git0.1.fc40.aarch64 15/54 Verifying : libb2-0.98.1-9.fc39.aarch64 16/54 Verifying : libmpc-1.3.1-3.fc39.aarch64 17/54 Verifying : libtool-ltdl-2.4.7-8.fc40.aarch64 18/54 Verifying : libxcrypt-devel-4.4.36-2.fc39.aarch64 19/54 Verifying : make-1:4.4.1-2.fc39.aarch64 20/54 Verifying : mpdecimal-2.5.1-7.fc39.aarch64 21/54 Verifying : pyproject-rpm-macros-1.9.0-2.fc39.noarch 22/54 Verifying : python-pip-wheel-23.2.1-1.fc39.noarch 23/54 Verifying : python-rpm-macros-3.12-4.fc40.noarch 24/54 Verifying : python3-3.12.0~rc2-1.fc40.aarch64 25/54 Verifying : python3-babel-2.12.1-4.fc39~bootstrap.noarch 26/54 Verifying : python3-charset-normalizer-3.2.0-2.fc39.noarch 27/54 Verifying : python3-cython-3.0.2-1.fc40.aarch64 28/54 Verifying : python3-devel-3.12.0~rc2-1.fc40.aarch64 29/54 Verifying : python3-docutils-0.20.1-1.fc40.noarch 30/54 Verifying : python3-idna-3.4-5.fc40.noarch 31/54 Verifying : python3-imagesize-1.4.1-5.fc40.noarch 32/54 Verifying : python3-jinja2-3.1.2-6.fc40.noarch 33/54 Verifying : python3-libs-3.12.0~rc2-1.fc40.aarch64 34/54 Verifying : python3-markupsafe-2.1.3-2.fc39.aarch64 35/54 Verifying : python3-packaging-23.1-5.fc40.noarch 36/54 Verifying : python3-pygments-2.16.1-1.fc40.noarch 37/54 Verifying : python3-pysocks-1.7.1-20.fc39.noarch 38/54 Verifying : python3-requests-2.28.2-6.fc40.noarch 39/54 Verifying : python3-rpm-generators-14-7.fc39.noarch 40/54 Verifying : python3-rpm-macros-3.12-4.fc40.noarch 41/54 Verifying : python3-setuptools-67.7.2-7.fc40.noarch 42/54 Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 43/54 Verifying : python3-sphinx-1:7.1.2-1.fc40.noarch 44/54 Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 45/54 Verifying : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 46/54 Verifying : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 47/54 Verifying : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 48/54 Verifying : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 49/54 Verifying : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 50/54 Verifying : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 51/54 Verifying : python3-urllib3+socks-1.26.16-3.fc40.noarch 52/54 Verifying : python3-urllib3-1.26.16-3.fc40.noarch 53/54 Verifying : xz-devel-5.4.4-1.fc39.aarch64 54/54 Installed: annobin-docs-12.26-1.fc40.noarch annobin-plugin-gcc-12.26-1.fc40.aarch64 bzip2-devel-1.0.8-16.fc39.aarch64 cpp-13.2.1-1.fc40.aarch64 expat-2.5.0-3.fc39.aarch64 gc-8.2.2-4.fc39.aarch64 gcc-13.2.1-1.fc40.aarch64 gcc-plugin-annobin-13.2.1-1.fc40.aarch64 glibc-devel-2.38.9000-8.fc40.aarch64 guile22-2.2.7-9.fc39.aarch64 kernel-headers-6.6.0-0.rc1.git0.1.fc40.aarch64 libasan-13.2.1-1.fc40.aarch64 libatomic-13.2.1-1.fc40.aarch64 libb2-0.98.1-9.fc39.aarch64 libmpc-1.3.1-3.fc39.aarch64 libtool-ltdl-2.4.7-8.fc40.aarch64 libubsan-13.2.1-1.fc40.aarch64 libxcrypt-devel-4.4.36-2.fc39.aarch64 make-1:4.4.1-2.fc39.aarch64 mpdecimal-2.5.1-7.fc39.aarch64 pyproject-rpm-macros-1.9.0-2.fc39.noarch python-pip-wheel-23.2.1-1.fc39.noarch python-rpm-macros-3.12-4.fc40.noarch python3-3.12.0~rc2-1.fc40.aarch64 python3-babel-2.12.1-4.fc39~bootstrap.noarch python3-charset-normalizer-3.2.0-2.fc39.noarch python3-cython-3.0.2-1.fc40.aarch64 python3-devel-3.12.0~rc2-1.fc40.aarch64 python3-docutils-0.20.1-1.fc40.noarch python3-idna-3.4-5.fc40.noarch python3-imagesize-1.4.1-5.fc40.noarch python3-jinja2-3.1.2-6.fc40.noarch python3-libs-3.12.0~rc2-1.fc40.aarch64 python3-markupsafe-2.1.3-2.fc39.aarch64 python3-packaging-23.1-5.fc40.noarch python3-pygments-2.16.1-1.fc40.noarch python3-pysocks-1.7.1-20.fc39.noarch python3-requests-2.28.2-6.fc40.noarch python3-rpm-generators-14-7.fc39.noarch python3-rpm-macros-3.12-4.fc40.noarch python3-setuptools-67.7.2-7.fc40.noarch python3-snowballstemmer-2.2.0-7.fc39.noarch python3-sphinx-1:7.1.2-1.fc40.noarch python3-sphinx-theme-alabaster-0.7.12-19.fc39.noarch python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarch python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch python3-sphinxcontrib-serializinghtml-1.1.5-10.fc39.noarch python3-urllib3-1.26.16-3.fc40.noarch python3-urllib3+socks-1.26.16-3.fc40.noarch xz-devel-5.4.4-1.fc39.aarch64 zlib-ng-compat-devel-2.1.3-3.fc40.aarch64 Complete! Finish: build setup for python-pysam-0.21.0-2.fc40.src.rpm Start: rpmbuild python-pysam-0.21.0-2.fc40.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1693872000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tQnfjg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.21.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.21.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.21.0 + rm -rf /builddir/build/BUILD/pysam-0.21.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/pysam-0.21.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcvcf.c pysam/libcutils.c pysam/libctabixproxies.c pysam/libctabix.c pysam/libcsamtools.c pysam/libcsamfile.c pysam/libchtslib.c pysam/libcfaidx.c pysam/libcbgzf.c pysam/libcbcftools.c pysam/libcbcf.c pysam/libcalignmentfile.c pysam/libcalignedsegment.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.iZSLiu + umask 022 + cd /builddir/build/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 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.21.0 + FORCE_CYTHON=1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' /builddir/build/BUILD/pysam-0.21.0/setup.py:435: SyntaxWarning: invalid escape sequence '\S' "#define (\S+)\s+(\S+)", line).groups() # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no checking whether C compiler accepts -mavx2... no checking whether C compiler accepts -mavx512f... no checking whether C compiler supports ARM Neon... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no checking whether C compiler accepts -mavx2... no checking whether C compiler accepts -mavx512f... no checking whether C compiler supports ARM Neon... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # pysam: htslib_config HTS_HAVE_NEON=yes # 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 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_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-aarch64-cpython-312 creating build/lib.linux-aarch64-cpython-312/pysam copying pysam/config.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-aarch64-cpython-312/pysam creating build/lib.linux-aarch64-cpython-312/pysam/include copying pysam/include/__init__.py -> build/lib.linux-aarch64-cpython-312/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing requirements to pysam.egg-info/requires.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _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/python3.12/site-packages/setuptools/command/build_py.py:201: _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/python3.12/site-packages/setuptools/command/build_py.py:201: _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/python3.12/site-packages/setuptools/command/build_py.py:201: _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/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-aarch64-cpython-312/pysam creating build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools creating build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools creating build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/README -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/configure -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/header.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/header.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/region.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.17"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -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 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_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 warning: pysam/libchtslib.pyx:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310 warning: pysam/libchtslib.pyx:40:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310 warning: pysam/libchtslib.pyx:41:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310 Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/htslib_util.c -o build/temp.linux-aarch64-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/htslib_util.o build/temp.linux-aarch64-cpython-312/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/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_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/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-aarch64-cpython-312/pysam/libchtslib.cpython-312-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-312/samtools creating build/temp.linux-aarch64-cpython-312/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-aarch64-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra.0’: samtools/bam_sort.c.pysam.c:2533:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2533 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2520:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2520 | char seq_[10000], *seq = seq_; | ^~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-aarch64-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcsamtools.o build/temp.linux-aarch64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/lz4/lz4.o build/temp.linux-aarch64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/samtools.pysam.o build/temp.linux-aarch64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2533:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2533 | seq[j] = comp[tmp]; | ^ samtools/bam_sort.c.pysam.c:2520:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2520 | char seq_[10000], *seq = seq_; | ^ Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-aarch64-cpython-312/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/hts.h:37, from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-aarch64-cpython-312/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-aarch64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcutils.o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcsamtools.cpython-312-aarch64-linux-gnu -lcbcftools.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcutils.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2582:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2631:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20430:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20430 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37151:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37151 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.cpython-312-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 -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-aarch64-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:35814:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35814 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libctabix.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbcf.c -o build/temp.linux-aarch64-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:86755:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86755 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:81419:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81419 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44519:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44519 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44545:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44545 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:81103:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81103 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-aarch64-cpython-312/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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/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/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcvcf.c -o build/temp.linux-aarch64-cpython-312/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:29574:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 29574 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24723:10: note: ‘__pyx_v_qual’ was declared here 24723 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.21.0/build/lib.linux-aarch64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.21.0/build/lib.linux-aarch64-cpython-312 + sphinx-build-3 doc html Running Sphinx v7.1.2 making output directory... done [autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst loading intersphinx inventory from https://docs.python.org/3.12/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.12/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.12/objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [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... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [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.ITHceT + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 + 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 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.21.0 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 --prefix /usr /builddir/build/BUILD/pysam-0.21.0/setup.py:435: SyntaxWarning: invalid escape sequence '\S' "#define (\S+)\s+(\S+)", line).groups() # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no checking whether C compiler accepts -mavx2... no checking whether C compiler accepts -mavx512f... no checking whether C compiler supports ARM Neon... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no checking whether C compiler accepts -mavx2... no checking whether C compiler accepts -mavx512f... no checking whether C compiler supports ARM Neon... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # pysam: htslib_config HTS_HAVE_NEON=yes # 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 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_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/ax_check_compile_flag.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include copying build/lib.linux-aarch64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam byte-compiling /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc writing byte-compilation script '/tmp/tmpl8r7a3iu.py' /usr/bin/python3 /tmp/tmpl8r7a3iu.py removing /tmp/tmpl8r7a3iu.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing requirements to pysam.egg-info/requires.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam-0.21.0-py3.12.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.21.0-2.fc40 --unique-debug-suffix -0.21.0-2.fc40.aarch64 --unique-debug-src-base python-pysam-0.21.0-2.fc40.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.21.0 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-0.21.0-2.fc40.aarch64 53110 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.21.0-2.fc40.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.EaPrF4 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python3-pysam + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.21.0/README.rst /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.iKXzCP + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.21.0/COPYING /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.21.0/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.21.0/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.21.0/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE Provides: bundled(bcftools) = 1.18 bundled(htslib) = 1.18 bundled(samtools) = 1.18 libcalignedsegment.cpython-312-aarch64-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-aarch64-linux-gnu.so()(64bit) libcbcf.cpython-312-aarch64-linux-gnu.so()(64bit) libcbcftools.cpython-312-aarch64-linux-gnu.so()(64bit) libcbgzf.cpython-312-aarch64-linux-gnu.so()(64bit) libcfaidx.cpython-312-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamfile.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so()(64bit) libctabix.cpython-312-aarch64-linux-gnu.so()(64bit) libctabixproxies.cpython-312-aarch64-linux-gnu.so()(64bit) libcutils.cpython-312-aarch64-linux-gnu.so()(64bit) libcvcf.cpython-312-aarch64-linux-gnu.so()(64bit) python-pysam = 0.21.0-2.fc40 python3-pysam = 0.21.0-2.fc40 python3-pysam(aarch-64) = 0.21.0-2.fc40 python3.12-pysam = 0.21.0-2.fc40 python3.12dist(pysam) = 0.21 python3dist(pysam) = 0.21 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) libcbcftools.cpython-312-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) python(abi) = 3.12 python3.12dist(cython) rtld(GNU_HASH) Obsoletes: python-pysam < 0.21.0-2.fc40 Processing files: python3-pysam-devel-0.21.0-2.fc40.aarch64 Provides: python-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel(aarch-64) = 0.21.0-2.fc40 python3.12-pysam-devel = 0.21.0-2.fc40 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) = 3.12 Processing files: python-pysam-doc-0.21.0-2.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FVeXIS + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python-pysam-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/pysam-0.21.0/html /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.21.0-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.21.0-2.fc40.aarch64 Provides: python-pysam-debugsource = 0.21.0-2.fc40 python-pysam-debugsource(aarch-64) = 0.21.0-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.21.0-2.fc40.aarch64 Provides: debuginfo(build-id) = 13b4567b4f784eaae96fbbd1ee54276fdc742555 debuginfo(build-id) = 2930a40a0e5c9d8097106d53301f4dc5e48f4184 debuginfo(build-id) = 2ec8e45dfefa70026cfd576fc30f30d3084182c8 debuginfo(build-id) = 38d5bbb0d2339d645d1dc64c0513711a51f5133f debuginfo(build-id) = 3fe81dfe259879c7d373b64095ee767c7f5336ba debuginfo(build-id) = 4896d2e89601ccffd7fce2884db58a008eb8cf2d debuginfo(build-id) = 7afcad80539aa4a001f4d7074bd1f12102bb54e3 debuginfo(build-id) = 9854b43751a14541e0ab0ec1da90244e3414cac0 debuginfo(build-id) = a73773d6722f84dc4b097433130adbe6e7356226 debuginfo(build-id) = a96f6a38541fb70f077970af3ff8ea77553d7781 debuginfo(build-id) = aff8b036bf132354bab9713c49d3771215abec9c debuginfo(build-id) = b55dfab7a74cee850a6261be6271d149fab9b382 debuginfo(build-id) = b9fb2f07bbb70def6f03dbffe5f671aee53e2915 libcalignedsegment.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcalignmentfile.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcbcf.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcbcftools.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcbgzf.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcfaidx.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcsamfile.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libctabix.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libctabixproxies.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcutils.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) libcvcf.cpython-312-aarch64-linux-gnu.so-0.21.0-2.fc40.aarch64.debug()(64bit) python-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo(aarch-64) = 0.21.0-2.fc40 python3.12-pysam-debuginfo = 0.21.0-2.fc40 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) = 0.21.0-2.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 Wrote: /builddir/build/RPMS/python3-pysam-0.21.0-2.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.21.0-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.21.0-2.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.21.0-2.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.21.0-2.fc40.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.21fUcz + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Ymb3K9 + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/pysam-0.21.0-SPECPARTS + rm -rf pysam-0.21.0 pysam-0.21.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: File listed twice: /usr/share/licenses/python3-pysam/LICENSE File listed twice: /usr/share/licenses/python3-pysam/LICENSE Finish: rpmbuild python-pysam-0.21.0-2.fc40.src.rpm Finish: build phase for python-pysam-0.21.0-2.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-aarch64-1694965618.485673/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.21.0-2.fc40.src.rpm) Config(child) 6 minutes 34 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python-pysam-debugsource", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "aarch64" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "aarch64" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "aarch64" }, { "name": "python-pysam", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "src" }, { "name": "python3-pysam", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "aarch64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "noarch" } ] } RPMResults finished