Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c108' (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-x86_64 --chroot fedora-rawhide-x86_64 Version: 0.69 PID: 5547 Logging PID: 5548 Task: {'appstream': False, 'background': True, 'build_id': 6407839, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', '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-x86_64/', '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-x86_64', '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-nz6lc9bc/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-nz6lc9bc/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-nz6lc9bc/python-pysam'... Running: git checkout df6b1de2eecf9ffcb551247d0ec58aa16cf5b345 -- cmd: ['git', 'checkout', 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-nz6lc9bc/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-nz6lc9bc/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 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 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 100 3957k 100 3957k 0 0 8869k 0 --:--:-- --:--:-- --:--:-- 8853k INFO: Reading stdout from command: md5sum pysam-0.21.0.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-nz6lc9bc/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nz6lc9bc/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1694963380.989643 -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-nz6lc9bc/python-pysam/python-pysam.spec) Config(fedora-rawhide-x86_64) 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-x86_64-bootstrap-1694963380.989643/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1694963380.989643/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/29d6a6de3359f20dd71427b54e81a63c0f0898edbf325ee22c8429ffc64c1a90/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/29d6a6de3359f20dd71427b54e81a63c0f0898edbf325ee22c8429ffc64c1a90/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 13 MB/s | 1.8 MB 00:00 fedora 27 MB/s | 73 MB 00:02 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 x86_64 1:1.14.10-1.fc40 fedora 155 k python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k python3-dbus x86_64 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 x86_64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.1 M Installed size: 3.5 M Downloading Packages: (1/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 180 kB/s | 157 kB 00:00 (2/7): dbus-libs-1.14.10-1.fc40.x86_64.rpm 152 kB/s | 155 kB 00:01 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 321 kB/s | 49 kB 00:00 (4/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 346 kB/s | 355 kB 00:01 (5/7): python3-dnf-plugins-core-4.4.2-1.fc39.no 1.1 MB/s | 293 kB 00:00 (6/7): python3-six-1.16.0-12.fc39.noarch.rpm 155 kB/s | 41 kB 00:00 (7/7): python3-systemd-235-5.fc39.x86_64.rpm 370 kB/s | 107 kB 00:00 -------------------------------------------------------------------------------- Total 848 kB/s | 1.1 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 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.x86_64 5/7 Installing : python3-dbus-1.3.2-4.fc39.x86_64 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.x86_64 1/7 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 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.x86_64 7/7 Installed: dbus-libs-1:1.14.10-1.fc40.x86_64 python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.x86_64 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.x86_64 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-x86_64-1694963380.989643/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 12 MB/s | 1.8 MB 00:00 fedora 21 MB/s | 73 MB 00:03 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.15-5.fc39 fedora 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.4-1.fc40 fedora 1.1 M cpio x86_64 2.14-4.fc39 fedora 279 k diffutils x86_64 3.10-3.fc39 fedora 398 k fedora-release-common noarch 40-0.7 fedora 18 k findutils x86_64 1:4.9.0-6.fc40 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38.9000-8.fc40 copr_base 73 k grep x86_64 3.11-5.fc40 fedora 298 k gzip x86_64 1.12-6.fc39 fedora 166 k info x86_64 7.0.3-3.fc39 fedora 182 k patch x86_64 2.7.6-22.fc39 fedora 125 k redhat-rpm-config noarch 270-1.fc40 copr_base 74 k rpm-build x86_64 4.18.99-1.fc40 fedora 78 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-1.fc40 fedora 1.3 M tar x86_64 2:1.35-2.fc40 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.2-1.fc40 fedora 1.2 M which x86_64 2.21-40.fc39 fedora 42 k xz x86_64 5.4.4-1.fc39 fedora 556 k Installing dependencies: alternatives x86_64 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs x86_64 3.1.2-4.fc40 fedora 117 k authselect x86_64 1.4.2-3.fc39 fedora 144 k authselect-libs x86_64 1.4.2-3.fc39 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.41-5.fc40 fedora 6.3 M binutils-gold x86_64 2.41-5.fc40 fedora 796 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-3.fc40 fedora 837 k coreutils-common x86_64 9.4-1.fc40 fedora 2.1 M cracklib x86_64 2.9.11-2.fc40 copr_base 83 k crypto-policies noarch 20230731-1.git5ed06e0.fc39 fedora 99 k curl x86_64 8.3.0-1.fc40 copr_base 354 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-10.fc39 fedora 77 k dwz x86_64 0.15-3.fc39 fedora 134 k ed x86_64 1.19-4.fc39 fedora 79 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils x86_64 0.189-6.fc40 fedora 535 k elfutils-debuginfod-client x86_64 0.189-6.fc40 fedora 38 k elfutils-default-yama-scope noarch 0.189-6.fc40 fedora 13 k elfutils-libelf x86_64 0.189-6.fc40 fedora 195 k elfutils-libs x86_64 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 x86_64 5.45-1.fc40 copr_base 50 k file-libs x86_64 5.45-1.fc40 copr_base 764 k filesystem x86_64 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 x86_64 13.2-8.fc40 fedora 4.2 M gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc x86_64 2.38.9000-8.fc40 copr_base 2.2 M glibc-common x86_64 2.38.9000-8.fc40 copr_base 350 k glibc-gconv-extra x86_64 2.38.9000-8.fc40 copr_base 1.6 M gmp x86_64 1:6.2.1-5.fc39 fedora 313 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 x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.1-7.fc39 fedora 31 k krb5-libs x86_64 1.21.2-1.fc40 fedora 765 k libacl x86_64 2.3.1-9.fc40 fedora 23 k libarchive x86_64 3.7.2-1.fc40 fedora 408 k libattr x86_64 2.5.1-9.fc40 fedora 18 k libblkid x86_64 2.39.2-1.fc40 fedora 116 k libbrotli x86_64 1.1.0-1.fc40 fedora 336 k libcap x86_64 2.48-7.fc39 fedora 68 k libcap-ng x86_64 0.8.3-8.fc40 fedora 32 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.3.0-1.fc40 copr_base 344 k libdb x86_64 5.3.28-58.fc40 copr_base 759 k libeconf x86_64 0.5.2-1.fc40 fedora 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.2-1.fc40 fedora 162 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.2.1-1.fc39 fedora 109 k libgomp x86_64 13.2.1-1.fc39 fedora 319 k libidn2 x86_64 2.3.4-3.fc39 fedora 117 k libmount x86_64 2.39.2-1.fc40 fedora 154 k libnghttp2 x86_64 1.56.0-1.fc40 fedora 75 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-6.fc39 fedora 120 k libselinux x86_64 3.5-5.fc39 fedora 87 k libsemanage x86_64 3.5-4.fc39 fedora 120 k libsepol x86_64 3.5-2.fc39 fedora 324 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.2-1.fc40 fedora 67 k libssh x86_64 0.10.5-2.fc39 fedora 211 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ x86_64 13.2.1-1.fc39 fedora 860 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.3-1.rc2.fc39 fedora 94 k libunistring x86_64 1.1-5.fc40 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.2-1.fc40 fedora 28 k libverto x86_64 0.3.2-6.fc39 fedora 20 k libxcrypt x86_64 4.4.36-2.fc39 fedora 119 k libxml2 x86_64 2.11.5-1.fc40 copr_base 697 k libzstd x86_64 1.5.5-4.fc40 copr_base 309 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.0-3.fc39 fedora 344 k ncurses-base noarch 6.4-7.20230520.fc40 fedora 88 k ncurses-libs x86_64 6.4-7.20230520.fc40 fedora 337 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.6-1.fc39 fedora 255 k openssl-libs x86_64 1:3.1.1-4.fc40 copr_base 2.2 M p11-kit x86_64 0.25.0-2.fc39 fedora 486 k p11-kit-trust x86_64 0.25.0-2.fc39 fedora 142 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-2.fc39 fedora 548 k pam-libs x86_64 1.5.3-2.fc39 fedora 58 k pcre2 x86_64 10.42-1.fc39.2 fedora 233 k pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf x86_64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config x86_64 1.9.5-2.fc39 fedora 9.6 k popt x86_64 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 x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.18.99-1.fc40 fedora 538 k rpm-build-libs x86_64 4.18.99-1.fc40 fedora 96 k rpm-libs x86_64 4.18.99-1.fc40 fedora 312 k rpm-sequoia x86_64 1.5.0-1.fc40 fedora 883 k rust-srpm-macros noarch 24-5.fc40 fedora 12 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs x86_64 3.43.1-1.fc40 fedora 688 k systemd-libs x86_64 254.1-2.fc40 fedora 688 k tzdata noarch 2023c-3.fc40 fedora 718 k util-linux-core x86_64 2.39.2-1.fc40 fedora 493 k xxhash-libs x86_64 0.8.2-1.fc39 fedora 37 k xz-libs x86_64 5.4.4-1.fc39 fedora 108 k zip x86_64 3.0-38.fc39 fedora 266 k zlib-ng-compat x86_64 2.1.3-3.fc40 copr_base 79 k zstd x86_64 1.5.5-4.fc40 copr_base 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 153 Packages Total download size: 53 M Installed size: 182 M Downloading Packages: (1/153): file-5.45-1.fc40.x86_64.rpm 872 kB/s | 50 kB 00:00 (2/153): cracklib-2.9.11-2.fc40.x86_64.rpm 896 kB/s | 83 kB 00:00 (3/153): curl-8.3.0-1.fc40.x86_64.rpm 2.0 MB/s | 354 kB 00:00 (4/153): file-libs-5.45-1.fc40.x86_64.rpm 5.5 MB/s | 764 kB 00:00 (5/153): glibc-2.38.9000-8.fc40.x86_64.rpm 11 MB/s | 2.2 MB 00:00 (6/153): glibc-common-2.38.9000-8.fc40.x86_64.r 3.2 MB/s | 350 kB 00:00 (7/153): glibc-gconv-extra-2.38.9000-8.fc40.x86 13 MB/s | 1.6 MB 00:00 (8/153): glibc-minimal-langpack-2.38.9000-8.fc4 2.1 MB/s | 73 kB 00:00 (9/153): libcurl-8.3.0-1.fc40.x86_64.rpm 9.2 MB/s | 344 kB 00:00 (10/153): libxml2-2.11.5-1.fc40.x86_64.rpm 27 MB/s | 697 kB 00:00 (11/153): libdb-5.3.28-58.fc40.x86_64.rpm 25 MB/s | 759 kB 00:00 (12/153): libzstd-1.5.5-4.fc40.x86_64.rpm 3.9 MB/s | 309 kB 00:00 (13/153): openssl-libs-3.1.1-4.fc40.x86_64.rpm 26 MB/s | 2.2 MB 00:00 (14/153): redhat-rpm-config-270-1.fc40.noarch.r 901 kB/s | 74 kB 00:00 (15/153): zlib-ng-compat-2.1.3-3.fc40.x86_64.rp 2.2 MB/s | 79 kB 00:00 (16/153): zstd-1.5.5-4.fc40.x86_64.rpm 31 MB/s | 482 kB 00:00 (17/153): ansible-srpm-macros-1-11.fc39.noarch. 197 kB/s | 21 kB 00:00 (18/153): alternatives-1.25-1.fc39.x86_64.rpm 335 kB/s | 39 kB 00:00 (19/153): audit-libs-3.1.2-4.fc40.x86_64.rpm 826 kB/s | 117 kB 00:00 (20/153): authselect-1.4.2-3.fc39.x86_64.rpm 2.0 MB/s | 144 kB 00:00 (21/153): basesystem-11-18.fc39.noarch.rpm 313 kB/s | 7.2 kB 00:00 (22/153): authselect-libs-1.4.2-3.fc39.x86_64.r 2.9 MB/s | 249 kB 00:00 (23/153): binutils-gold-2.41-5.fc40.x86_64.rpm 11 MB/s | 796 kB 00:00 (24/153): bash-5.2.15-5.fc39.x86_64.rpm 15 MB/s | 1.8 MB 00:00 (25/153): bzip2-1.0.8-16.fc39.x86_64.rpm 1.7 MB/s | 52 kB 00:00 (26/153): bzip2-libs-1.0.8-16.fc39.x86_64.rpm 1.6 MB/s | 41 kB 00:00 (27/153): coreutils-9.4-1.fc40.x86_64.rpm 16 MB/s | 1.1 MB 00:00 (28/153): binutils-2.41-5.fc40.x86_64.rpm 27 MB/s | 6.3 MB 00:00 (29/153): ca-certificates-2023.2.60_v7.0.306-3. 6.9 MB/s | 837 kB 00:00 (30/153): cpio-2.14-4.fc39.x86_64.rpm 10 MB/s | 279 kB 00:00 (31/153): crypto-policies-20230731-1.git5ed06e0 3.9 MB/s | 99 kB 00:00 (32/153): coreutils-common-9.4-1.fc40.x86_64.rp 37 MB/s | 2.1 MB 00:00 (33/153): 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00:00 (150/153): xxhash-libs-0.8.2-1.fc39.x86_64.rpm 1.7 MB/s | 37 kB 00:00 (151/153): xz-5.4.4-1.fc39.x86_64.rpm 20 MB/s | 556 kB 00:00 (152/153): xz-libs-5.4.4-1.fc39.x86_64.rpm 4.3 MB/s | 108 kB 00:00 (153/153): zip-3.0-38.fc39.x86_64.rpm 11 MB/s | 266 kB 00:00 -------------------------------------------------------------------------------- Total 26 MB/s | 53 MB 00:02 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.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-1.fc39.x86_64 1/153 Running scriptlet: libgcc-13.2.1-1.fc39.x86_64 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.x86_64 11/153 Installing : basesystem-11-18.fc39.noarch 12/153 Installing : rust-srpm-macros-24-5.fc40.noarch 13/153 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grep-3.11-5.fc40.x86_64 67/153 Installing : findutils-1:4.9.0-6.fc40.x86_64 68/153 Installing : xz-5.4.4-1.fc39.x86_64 69/153 Installing : libmount-2.39.2-1.fc40.x86_64 70/153 Installing : util-linux-core-2.39.2-1.fc40.x86_64 71/153 Installing : libsemanage-3.5-4.fc39.x86_64 72/153 Installing : tar-2:1.35-2.fc40.x86_64 73/153 Installing : libpsl-0.21.2-4.fc39.x86_64 74/153 Installing : zip-3.0-38.fc39.x86_64 75/153 Installing : zstd-1.5.5-4.fc40.x86_64 76/153 Installing : libfdisk-2.39.2-1.fc40.x86_64 77/153 Installing : bzip2-1.0.8-16.fc39.x86_64 78/153 Installing : libxml2-2.11.5-1.fc40.x86_64 79/153 Installing : sqlite-libs-3.43.1-1.fc40.x86_64 80/153 Installing : ed-1.19-4.fc39.x86_64 81/153 Installing : patch-2.7.6-22.fc39.x86_64 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.x86_64 84/153 Installing : cpio-2.14-4.fc39.x86_64 85/153 Installing : diffutils-3.10-3.fc39.x86_64 86/153 Installing : gdbm-libs-1:1.23-4.fc39.x86_64 87/153 Installing : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 88/153 Installing : keyutils-libs-1.6.1-7.fc39.x86_64 89/153 Installing : libbrotli-1.1.0-1.fc40.x86_64 90/153 Installing : libeconf-0.5.2-1.fc40.x86_64 91/153 Installing : shadow-utils-2:4.14.0-1.fc40.x86_64 92/153 Running scriptlet: libutempter-1.2.1-10.fc39.x86_64 93/153 Installing : libutempter-1.2.1-10.fc39.x86_64 93/153 Installing : libffi-3.4.4-4.fc39.x86_64 94/153 Installing : p11-kit-0.25.0-2.fc39.x86_64 95/153 Installing : libgomp-13.2.1-1.fc39.x86_64 96/153 Installing : libnghttp2-1.56.0-1.fc40.x86_64 97/153 Installing : libpkgconf-1.9.5-2.fc39.x86_64 98/153 Installing : pkgconf-1.9.5-2.fc39.x86_64 99/153 Installing : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 100/153 Installing : libsigsegv-2.14-5.fc39.x86_64 101/153 Installing : gawk-5.2.2-2.fc39.x86_64 102/153 Installing : libtasn1-4.19.0-3.fc39.x86_64 103/153 Installing : p11-kit-trust-0.25.0-2.fc39.x86_64 104/153 Running scriptlet: p11-kit-trust-0.25.0-2.fc39.x86_64 104/153 Installing : libverto-0.3.2-6.fc39.x86_64 105/153 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 106/153 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.x86_64 112/153 Installing : openssl-libs-1:3.1.1-4.fc40.x86_64 113/153 Installing : coreutils-9.4-1.fc40.x86_64 114/153 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.x86_64 116/153 Installing : libtirpc-1.3.3-1.rc2.fc39.x86_64 117/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.x86_64 118/153 Installing : authselect-libs-1.4.2-3.fc39.x86_64 118/153 Installing : gzip-1.12-6.fc39.x86_64 119/153 Installing : cracklib-2.9.11-2.fc40.x86_64 120/153 Installing : libpwquality-1.4.5-6.fc39.x86_64 121/153 Installing : authselect-1.4.2-3.fc39.x86_64 122/153 Installing : libnsl2-2.0.0-6.fc39.x86_64 123/153 Installing : pam-1.5.3-2.fc39.x86_64 124/153 Installing : libssh-0.10.5-2.fc39.x86_64 125/153 Installing : libarchive-3.7.2-1.fc40.x86_64 126/153 Installing : libevent-2.1.12-9.fc39.x86_64 127/153 Installing : openldap-2.6.6-1.fc39.x86_64 128/153 Installing : libcurl-8.3.0-1.fc40.x86_64 129/153 Installing : elfutils-debuginfod-client-0.189-6.fc40.x86_64 130/153 Installing : elfutils-libs-0.189-6.fc40.x86_64 131/153 Installing : binutils-gold-2.41-5.fc40.x86_64 132/153 Running scriptlet: binutils-gold-2.41-5.fc40.x86_64 132/153 Installing : binutils-2.41-5.fc40.x86_64 133/153 Running scriptlet: binutils-2.41-5.fc40.x86_64 133/153 Installing : elfutils-0.189-6.fc40.x86_64 134/153 Installing : gdb-minimal-13.2-8.fc40.x86_64 135/153 Installing : debugedit-5.0-10.fc39.x86_64 136/153 Installing : curl-8.3.0-1.fc40.x86_64 137/153 Installing : rpm-sequoia-1.5.0-1.fc40.x86_64 138/153 Installing : rpm-libs-4.18.99-1.fc40.x86_64 139/153 Running scriptlet: rpm-4.18.99-1.fc40.x86_64 140/153 Installing : rpm-4.18.99-1.fc40.x86_64 140/153 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.x86_64 143/153 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.x86_64 150/153 Installing : util-linux-2.39.2-1.fc40.x86_64 151/153 Installing : which-2.21-40.fc39.x86_64 152/153 Installing : info-7.0.3-3.fc39.x86_64 153/153 Running scriptlet: filesystem-3.18-6.fc39.x86_64 153/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.x86_64 153/153 Running scriptlet: rpm-4.18.99-1.fc40.x86_64 153/153 Running scriptlet: info-7.0.3-3.fc39.x86_64 153/153 Verifying : cracklib-2.9.11-2.fc40.x86_64 1/153 Verifying : curl-8.3.0-1.fc40.x86_64 2/153 Verifying : file-5.45-1.fc40.x86_64 3/153 Verifying : file-libs-5.45-1.fc40.x86_64 4/153 Verifying : glibc-2.38.9000-8.fc40.x86_64 5/153 Verifying : glibc-common-2.38.9000-8.fc40.x86_64 6/153 Verifying : glibc-gconv-extra-2.38.9000-8.fc40.x86_64 7/153 Verifying : glibc-minimal-langpack-2.38.9000-8.fc40.x86_64 8/153 Verifying : libcurl-8.3.0-1.fc40.x86_64 9/153 Verifying : libdb-5.3.28-58.fc40.x86_64 10/153 Verifying : libxml2-2.11.5-1.fc40.x86_64 11/153 Verifying : libzstd-1.5.5-4.fc40.x86_64 12/153 Verifying : openssl-libs-1:3.1.1-4.fc40.x86_64 13/153 Verifying : redhat-rpm-config-270-1.fc40.noarch 14/153 Verifying : zlib-ng-compat-2.1.3-3.fc40.x86_64 15/153 Verifying : zstd-1.5.5-4.fc40.x86_64 16/153 Verifying : alternatives-1.25-1.fc39.x86_64 17/153 Verifying : ansible-srpm-macros-1-11.fc39.noarch 18/153 Verifying : audit-libs-3.1.2-4.fc40.x86_64 19/153 Verifying : authselect-1.4.2-3.fc39.x86_64 20/153 Verifying : authselect-libs-1.4.2-3.fc39.x86_64 21/153 Verifying : basesystem-11-18.fc39.noarch 22/153 Verifying : bash-5.2.15-5.fc39.x86_64 23/153 Verifying : binutils-2.41-5.fc40.x86_64 24/153 Verifying : binutils-gold-2.41-5.fc40.x86_64 25/153 Verifying : bzip2-1.0.8-16.fc39.x86_64 26/153 Verifying : bzip2-libs-1.0.8-16.fc39.x86_64 27/153 Verifying : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 28/153 Verifying : coreutils-9.4-1.fc40.x86_64 29/153 Verifying : coreutils-common-9.4-1.fc40.x86_64 30/153 Verifying : cpio-2.14-4.fc39.x86_64 31/153 Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 32/153 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 33/153 Verifying : debugedit-5.0-10.fc39.x86_64 34/153 Verifying : diffutils-3.10-3.fc39.x86_64 35/153 Verifying : dwz-0.15-3.fc39.x86_64 36/153 Verifying : ed-1.19-4.fc39.x86_64 37/153 Verifying : efi-srpm-macros-5-9.fc39.noarch 38/153 Verifying : elfutils-0.189-6.fc40.x86_64 39/153 Verifying : elfutils-debuginfod-client-0.189-6.fc40.x86_64 40/153 Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 41/153 Verifying : elfutils-libelf-0.189-6.fc40.x86_64 42/153 Verifying : elfutils-libs-0.189-6.fc40.x86_64 43/153 Verifying : fedora-gpg-keys-40-0.1.noarch 44/153 Verifying : fedora-release-40-0.7.noarch 45/153 Verifying : fedora-release-common-40-0.7.noarch 46/153 Verifying : fedora-release-identity-basic-40-0.7.noarch 47/153 Verifying : fedora-repos-40-0.1.noarch 48/153 Verifying : fedora-repos-rawhide-40-0.1.noarch 49/153 Verifying : filesystem-3.18-6.fc39.x86_64 50/153 Verifying : findutils-1:4.9.0-6.fc40.x86_64 51/153 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 52/153 Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 53/153 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 54/153 Verifying : gawk-5.2.2-2.fc39.x86_64 55/153 Verifying : gdb-minimal-13.2-8.fc40.x86_64 56/153 Verifying : gdbm-libs-1:1.23-4.fc39.x86_64 57/153 Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 58/153 Verifying : gmp-1:6.2.1-5.fc39.x86_64 59/153 Verifying : gnat-srpm-macros-6-3.fc39.noarch 60/153 Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 61/153 Verifying : grep-3.11-5.fc40.x86_64 62/153 Verifying : gzip-1.12-6.fc39.x86_64 63/153 Verifying : info-7.0.3-3.fc39.x86_64 64/153 Verifying : jansson-2.13.1-7.fc39.x86_64 65/153 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 66/153 Verifying : keyutils-libs-1.6.1-7.fc39.x86_64 67/153 Verifying : krb5-libs-1.21.2-1.fc40.x86_64 68/153 Verifying : libacl-2.3.1-9.fc40.x86_64 69/153 Verifying : libarchive-3.7.2-1.fc40.x86_64 70/153 Verifying : libattr-2.5.1-9.fc40.x86_64 71/153 Verifying : libblkid-2.39.2-1.fc40.x86_64 72/153 Verifying : libbrotli-1.1.0-1.fc40.x86_64 73/153 Verifying : libcap-2.48-7.fc39.x86_64 74/153 Verifying : libcap-ng-0.8.3-8.fc40.x86_64 75/153 Verifying : libcom_err-1.47.0-2.fc39.x86_64 76/153 Verifying : libeconf-0.5.2-1.fc40.x86_64 77/153 Verifying : libevent-2.1.12-9.fc39.x86_64 78/153 Verifying : libfdisk-2.39.2-1.fc40.x86_64 79/153 Verifying : libffi-3.4.4-4.fc39.x86_64 80/153 Verifying : libgcc-13.2.1-1.fc39.x86_64 81/153 Verifying : libgomp-13.2.1-1.fc39.x86_64 82/153 Verifying : libidn2-2.3.4-3.fc39.x86_64 83/153 Verifying : libmount-2.39.2-1.fc40.x86_64 84/153 Verifying : libnghttp2-1.56.0-1.fc40.x86_64 85/153 Verifying : libnsl2-2.0.0-6.fc39.x86_64 86/153 Verifying : libpkgconf-1.9.5-2.fc39.x86_64 87/153 Verifying : libpsl-0.21.2-4.fc39.x86_64 88/153 Verifying : libpwquality-1.4.5-6.fc39.x86_64 89/153 Verifying : libselinux-3.5-5.fc39.x86_64 90/153 Verifying : libsemanage-3.5-4.fc39.x86_64 91/153 Verifying : libsepol-3.5-2.fc39.x86_64 92/153 Verifying : libsigsegv-2.14-5.fc39.x86_64 93/153 Verifying : libsmartcols-2.39.2-1.fc40.x86_64 94/153 Verifying : libssh-0.10.5-2.fc39.x86_64 95/153 Verifying : libssh-config-0.10.5-2.fc39.noarch 96/153 Verifying : libstdc++-13.2.1-1.fc39.x86_64 97/153 Verifying : libtasn1-4.19.0-3.fc39.x86_64 98/153 Verifying : libtirpc-1.3.3-1.rc2.fc39.x86_64 99/153 Verifying : libunistring-1.1-5.fc40.x86_64 100/153 Verifying : libutempter-1.2.1-10.fc39.x86_64 101/153 Verifying : libuuid-2.39.2-1.fc40.x86_64 102/153 Verifying : libverto-0.3.2-6.fc39.x86_64 103/153 Verifying : libxcrypt-4.4.36-2.fc39.x86_64 104/153 Verifying : lua-libs-5.4.6-3.fc39.x86_64 105/153 Verifying : lua-srpm-macros-1-9.fc39.noarch 106/153 Verifying : lz4-libs-1.9.4-4.fc39.x86_64 107/153 Verifying : mpfr-4.2.0-3.fc39.x86_64 108/153 Verifying : ncurses-base-6.4-7.20230520.fc40.noarch 109/153 Verifying : ncurses-libs-6.4-7.20230520.fc40.x86_64 110/153 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.x86_64 113/153 Verifying : p11-kit-0.25.0-2.fc39.x86_64 114/153 Verifying : p11-kit-trust-0.25.0-2.fc39.x86_64 115/153 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 116/153 Verifying : pam-1.5.3-2.fc39.x86_64 117/153 Verifying : pam-libs-1.5.3-2.fc39.x86_64 118/153 Verifying : patch-2.7.6-22.fc39.x86_64 119/153 Verifying : pcre2-10.42-1.fc39.2.x86_64 120/153 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.x86_64 123/153 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 124/153 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 125/153 Verifying : popt-1.19-3.fc39.x86_64 126/153 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.x86_64 132/153 Verifying : rpm-4.18.99-1.fc40.x86_64 133/153 Verifying : rpm-build-4.18.99-1.fc40.x86_64 134/153 Verifying : rpm-build-libs-4.18.99-1.fc40.x86_64 135/153 Verifying : rpm-libs-4.18.99-1.fc40.x86_64 136/153 Verifying : rpm-sequoia-1.5.0-1.fc40.x86_64 137/153 Verifying : rust-srpm-macros-24-5.fc40.noarch 138/153 Verifying : sed-4.8-14.fc39.x86_64 139/153 Verifying : setup-2.14.4-1.fc39.noarch 140/153 Verifying : shadow-utils-2:4.14.0-1.fc40.x86_64 141/153 Verifying : sqlite-libs-3.43.1-1.fc40.x86_64 142/153 Verifying : systemd-libs-254.1-2.fc40.x86_64 143/153 Verifying : tar-2:1.35-2.fc40.x86_64 144/153 Verifying : tzdata-2023c-3.fc40.noarch 145/153 Verifying : unzip-6.0-62.fc39.x86_64 146/153 Verifying : util-linux-2.39.2-1.fc40.x86_64 147/153 Verifying : util-linux-core-2.39.2-1.fc40.x86_64 148/153 Verifying : which-2.21-40.fc39.x86_64 149/153 Verifying : xxhash-libs-0.8.2-1.fc39.x86_64 150/153 Verifying : xz-5.4.4-1.fc39.x86_64 151/153 Verifying : xz-libs-5.4.4-1.fc39.x86_64 152/153 Verifying : zip-3.0-38.fc39.x86_64 153/153 Installed: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.x86_64 authselect-1.4.2-3.fc39.x86_64 authselect-libs-1.4.2-3.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.x86_64 binutils-2.41-5.fc40.x86_64 binutils-gold-2.41-5.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc40.x86_64 crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-10.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.x86_64 elfutils-debuginfod-client-0.189-6.fc40.x86_64 elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.x86_64 elfutils-libs-0.189-6.fc40.x86_64 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.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-6.fc40.x86_64 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.x86_64 gdb-minimal-13.2-8.fc40.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.x86_64 glibc-common-2.38.9000-8.fc40.x86_64 glibc-gconv-extra-2.38.9000-8.fc40.x86_64 glibc-minimal-langpack-2.38.9000-8.fc40.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-7.fc40.noarch grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-1.fc40.x86_64 libacl-2.3.1-9.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.48-7.fc39.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.3.0-1.fc40.x86_64 libdb-5.3.28-58.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-1.fc39.x86_64 libgomp-13.2.1-1.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.56.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.3-1.rc2.fc39.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.11.5-1.fc40.x86_64 libzstd-1.5.5-4.fc40.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.1-4.fc40.x86_64 p11-kit-0.25.0-2.fc39.x86_64 p11-kit-trust-0.25.0-2.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.x86_64 pam-libs-1.5.3-2.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 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.x86_64 redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.x86_64 rpm-build-4.18.99-1.fc40.x86_64 rpm-build-libs-4.18.99-1.fc40.x86_64 rpm-libs-4.18.99-1.fc40.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-1.fc40.x86_64 sqlite-libs-3.43.1-1.fc40.x86_64 systemd-libs-254.1-2.fc40.x86_64 tar-2:1.35-2.fc40.x86_64 tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-38.fc39.x86_64 zlib-ng-compat-2.1.3-3.fc40.x86_64 zstd-1.5.5-4.fc40.x86_64 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.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.x86_64 authselect-1.4.2-3.fc39.x86_64 authselect-libs-1.4.2-3.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.x86_64 binutils-2.41-5.fc40.x86_64 binutils-gold-2.41-5.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc40.x86_64 crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-10.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.x86_64 elfutils-debuginfod-client-0.189-6.fc40.x86_64 elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.x86_64 elfutils-libs-0.189-6.fc40.x86_64 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.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-6.fc40.x86_64 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.x86_64 gdb-minimal-13.2-8.fc40.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.x86_64 glibc-common-2.38.9000-8.fc40.x86_64 glibc-gconv-extra-2.38.9000-8.fc40.x86_64 glibc-minimal-langpack-2.38.9000-8.fc40.x86_64 gmp-6.2.1-5.fc39.x86_64 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.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-1.fc40.x86_64 libacl-2.3.1-9.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.48-7.fc39.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.3.0-1.fc40.x86_64 libdb-5.3.28-58.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-1.fc39.x86_64 libgomp-13.2.1-1.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.56.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.3-1.rc2.fc39.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.11.5-1.fc40.x86_64 libzstd-1.5.5-4.fc40.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.1-4.fc40.x86_64 p11-kit-0.25.0-2.fc39.x86_64 p11-kit-trust-0.25.0-2.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.x86_64 pam-libs-1.5.3-2.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 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.x86_64 redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.x86_64 rpm-build-4.18.99-1.fc40.x86_64 rpm-build-libs-4.18.99-1.fc40.x86_64 rpm-libs-4.18.99-1.fc40.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-1.fc40.x86_64 sqlite-libs-3.43.1-1.fc40.x86_64 systemd-libs-254.1-2.fc40.x86_64 tar-1.35-2.fc40.x86_64 tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-38.fc39.x86_64 zlib-ng-compat-2.1.3-3.fc40.x86_64 zstd-1.5.5-4.fc40.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 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-x86_64-1694963380.989643/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1694963380.989643/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1694963380.989643/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-nz6lc9bc/python-pysam/python-pysam.spec) Config(child) 1 minutes 19 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-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1694963380.989643/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1694963380.989643/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1694963380.989643/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.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 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: x86_64 Building for target x86_64 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 33 kB/s | 1.5 kB 00:00 fedora 179 kB/s | 7.8 kB 00:00 Dependencies resolved. ========================================================================================= Package Arch Version Repo Size ========================================================================================= Installing: bzip2-devel x86_64 1.0.8-16.fc39 fedora 214 k gcc x86_64 13.2.1-1.fc39 fedora 34 M python3-cython x86_64 3.0.2-1.fc40 fedora 3.8 M python3-devel x86_64 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 x86_64 5.4.4-1.fc39 fedora 66 k zlib-ng-compat-devel x86_64 2.1.3-3.fc40 copr_base 34 k Installing dependencies: annobin-docs noarch 12.26-1.fc40 fedora 94 k annobin-plugin-gcc x86_64 12.26-1.fc40 fedora 958 k cpp x86_64 13.2.1-1.fc39 fedora 11 M expat x86_64 2.5.0-3.fc39 fedora 110 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc-plugin-annobin x86_64 13.2.1-1.fc39 fedora 47 k glibc-devel x86_64 2.38.9000-8.fc40 copr_base 84 k glibc-headers-x86 noarch 2.38.9000-8.fc40 copr_base 497 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M kernel-headers x86_64 6.6.0-0.rc1.git0.1.fc40 fedora 1.6 M libb2 x86_64 0.98.1-9.fc39 fedora 25 k libmpc x86_64 1.3.1-3.fc39 fedora 70 k libtool-ltdl x86_64 2.4.7-8.fc40 fedora 36 k libxcrypt-devel x86_64 4.4.36-2.fc39 fedora 30 k make x86_64 1:4.4.1-2.fc39 fedora 589 k mpdecimal x86_64 2.5.1-7.fc39 fedora 89 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 x86_64 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 x86_64 3.12.0~rc2-1.fc40 fedora 9.2 M python3-markupsafe x86_64 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 52 Packages Total download size: 87 M Installed size: 316 M Downloading Packages: (1/52): glibc-devel-2.38.9000-8.fc40.x86_64.rpm 1.8 MB/s | 84 kB 00:00 (2/52): zlib-ng-compat-devel-2.1.3-3.fc40.x86_6 715 kB/s | 34 kB 00:00 (3/52): glibc-headers-x86-2.38.9000-8.fc40.noar 6.6 MB/s | 497 kB 00:00 (4/52): annobin-docs-12.26-1.fc40.noarch.rpm 828 kB/s | 94 kB 00:00 (5/52): bzip2-devel-1.0.8-16.fc39.x86_64.rpm 1.5 MB/s | 214 kB 00:00 (6/52): annobin-plugin-gcc-12.26-1.fc40.x86_64. 4.8 MB/s | 958 kB 00:00 (7/52): expat-2.5.0-3.fc39.x86_64.rpm 3.7 MB/s | 110 kB 00:00 (8/52): gc-8.2.2-4.fc39.x86_64.rpm 3.9 MB/s | 110 kB 00:00 (9/52): gcc-plugin-annobin-13.2.1-1.fc39.x86_64 1.4 MB/s | 47 kB 00:00 (10/52): cpp-13.2.1-1.fc39.x86_64.rpm 22 MB/s | 11 MB 00:00 (11/52): guile22-2.2.7-9.fc39.x86_64.rpm 18 MB/s | 6.5 MB 00:00 (12/52): libb2-0.98.1-9.fc39.x86_64.rpm 616 kB/s | 25 kB 00:00 (13/52): libmpc-1.3.1-3.fc39.x86_64.rpm 1.2 MB/s | 70 kB 00:00 (14/52): libtool-ltdl-2.4.7-8.fc40.x86_64.rpm 934 kB/s | 36 kB 00:00 (15/52): libxcrypt-devel-4.4.36-2.fc39.x86_64.r 1.2 MB/s | 30 kB 00:00 (16/52): kernel-headers-6.6.0-0.rc1.git0.1.fc40 7.4 MB/s | 1.6 MB 00:00 (17/52): make-4.4.1-2.fc39.x86_64.rpm 9.4 MB/s | 589 kB 00:00 (18/52): mpdecimal-2.5.1-7.fc39.x86_64.rpm 2.2 MB/s | 89 kB 00:00 (19/52): pyproject-rpm-macros-1.9.0-2.fc39.noar 1.1 MB/s | 41 kB 00:00 (20/52): python-rpm-macros-3.12-4.fc40.noarch.r 295 kB/s | 19 kB 00:00 (21/52): python3-3.12.0~rc2-1.fc40.x86_64.rpm 676 kB/s | 26 kB 00:00 (22/52): python-pip-wheel-23.2.1-1.fc39.noarch. 10 MB/s | 1.5 MB 00:00 (23/52): python3-charset-normalizer-3.2.0-2.fc3 4.1 MB/s | 105 kB 00:00 (24/52): gcc-13.2.1-1.fc39.x86_64.rpm 36 MB/s | 34 MB 00:00 (25/52): python3-babel-2.12.1-4.fc39~bootstrap. 24 MB/s | 6.9 MB 00:00 (26/52): python3-devel-3.12.0~rc2-1.fc40.x86_64 506 kB/s | 311 kB 00:00 (27/52): python3-docutils-0.20.1-1.fc40.noarch. 2.0 MB/s | 1.0 MB 00:00 (28/52): python3-imagesize-1.4.1-5.fc40.noarch. 1.3 MB/s | 22 kB 00:00 (29/52): python3-cython-3.0.2-1.fc40.x86_64.rpm 4.3 MB/s | 3.8 MB 00:00 (30/52): python3-jinja2-3.1.2-6.fc40.noarch.rpm 5.9 MB/s | 505 kB 00:00 (31/52): python3-markupsafe-2.1.3-2.fc39.x86_64 1.4 MB/s | 30 kB 00:00 (32/52): python3-packaging-23.1-5.fc40.noarch.r 5.4 MB/s | 115 kB 00:00 (33/52): python3-pygments-2.16.1-1.fc40.noarch. 20 MB/s | 2.4 MB 00:00 (34/52): python3-idna-3.4-5.fc40.noarch.rpm 336 kB/s | 109 kB 00:00 (35/52): python3-requests-2.28.2-6.fc40.noarch. 3.5 MB/s | 151 kB 00:00 (36/52): python3-libs-3.12.0~rc2-1.fc40.x86_64. 39 MB/s | 9.2 MB 00:00 (37/52): python3-pysocks-1.7.1-20.fc39.noarch.r 550 kB/s | 39 kB 00:00 (38/52): python3-rpm-generators-14-7.fc39.noarc 1.1 MB/s | 30 kB 00:00 (39/52): python3-rpm-macros-3.12-4.fc40.noarch. 497 kB/s | 14 kB 00:00 (40/52): python3-snowballstemmer-2.2.0-7.fc39.n 6.6 MB/s | 257 kB 00:00 (41/52): python3-sphinx-theme-alabaster-0.7.12- 641 kB/s | 29 kB 00:00 (42/52): python3-setuptools-67.7.2-7.fc40.noarc 15 MB/s | 1.5 MB 00:00 (43/52): python3-sphinx-7.1.2-1.fc40.noarch.rpm 27 MB/s | 2.6 MB 00:00 (44/52): python3-sphinxcontrib-applehelp-1.0.6- 1.8 MB/s | 45 kB 00:00 (45/52): python3-sphinxcontrib-devhelp-1.0.2-14 2.0 MB/s | 41 kB 00:00 (46/52): python3-sphinxcontrib-htmlhelp-2.0.3-1 2.3 MB/s | 54 kB 00:00 (47/52): python3-sphinxcontrib-jsmath-1.0.1-22. 739 kB/s | 17 kB 00:00 (48/52): python3-sphinxcontrib-qthelp-1.0.3-15. 2.0 MB/s | 47 kB 00:00 (49/52): python3-sphinxcontrib-serializinghtml- 2.6 MB/s | 47 kB 00:00 (50/52): python3-urllib3+socks-1.26.16-3.fc40.n 538 kB/s | 9.9 kB 00:00 (51/52): python3-urllib3-1.26.16-3.fc40.noarch. 11 MB/s | 273 kB 00:00 (52/52): xz-devel-5.4.4-1.fc39.x86_64.rpm 3.7 MB/s | 66 kB 00:00 -------------------------------------------------------------------------------- Total 36 MB/s | 87 MB 00:02 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 1/52 Installing : python3-rpm-macros-3.12-4.fc40.noarch 2/52 Installing : libmpc-1.3.1-3.fc39.x86_64 3/52 Installing : cpp-13.2.1-1.fc39.x86_64 4/52 Installing : pyproject-rpm-macros-1.9.0-2.fc39.noarch 5/52 Installing : python-pip-wheel-23.2.1-1.fc39.noarch 6/52 Installing : mpdecimal-2.5.1-7.fc39.x86_64 7/52 Installing : libtool-ltdl-2.4.7-8.fc40.x86_64 8/52 Installing : libb2-0.98.1-9.fc39.x86_64 9/52 Installing : kernel-headers-6.6.0-0.rc1.git0.1.fc40.x86_64 10/52 Installing : gc-8.2.2-4.fc39.x86_64 11/52 Installing : guile22-2.2.7-9.fc39.x86_64 12/52 Installing : make-1:4.4.1-2.fc39.x86_64 13/52 Installing : expat-2.5.0-3.fc39.x86_64 14/52 Installing : python3-3.12.0~rc2-1.fc40.x86_64 15/52 Installing : python3-libs-3.12.0~rc2-1.fc40.x86_64 16/52 Installing : python3-idna-3.4-5.fc40.noarch 17/52 Installing : python3-packaging-23.1-5.fc40.noarch 18/52 Installing : python3-rpm-generators-14-7.fc39.noarch 19/52 Installing : python3-babel-2.12.1-4.fc39~bootstrap.noarch 20/52 Installing : python3-charset-normalizer-3.2.0-2.fc39.noarch 21/52 Installing : python3-docutils-0.20.1-1.fc40.noarch 22/52 Installing : python3-imagesize-1.4.1-5.fc40.noarch 23/52 Installing : python3-markupsafe-2.1.3-2.fc39.x86_64 24/52 Installing : python3-jinja2-3.1.2-6.fc40.noarch 25/52 Installing : python3-pygments-2.16.1-1.fc40.noarch 26/52 Installing : python3-pysocks-1.7.1-20.fc39.noarch 27/52 Installing : python3-urllib3+socks-1.26.16-3.fc40.noarch 28/52 Installing : python3-urllib3-1.26.16-3.fc40.noarch 29/52 Installing : python3-requests-2.28.2-6.fc40.noarch 30/52 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 31/52 Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 32/52 Installing : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 33/52 Installing : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 34/52 Installing : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 35/52 Installing : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 36/52 Installing : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 37/52 Installing : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 38/52 Installing : python3-sphinx-1:7.1.2-1.fc40.noarch 39/52 Installing : annobin-docs-12.26-1.fc40.noarch 40/52 Installing : glibc-headers-x86-2.38.9000-8.fc40.noarch 41/52 Installing : libxcrypt-devel-4.4.36-2.fc39.x86_64 42/52 Installing : glibc-devel-2.38.9000-8.fc40.x86_64 43/52 Installing : gcc-13.2.1-1.fc39.x86_64 44/52 Running scriptlet: gcc-13.2.1-1.fc39.x86_64 44/52 Installing : annobin-plugin-gcc-12.26-1.fc40.x86_64 45/52 Running scriptlet: annobin-plugin-gcc-12.26-1.fc40.x86_64 45/52 Installing : gcc-plugin-annobin-13.2.1-1.fc39.x86_64 46/52 Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc39.x86_64 46/52 Installing : python3-devel-3.12.0~rc2-1.fc40.x86_64 47/52 Installing : python3-cython-3.0.2-1.fc40.x86_64 48/52 Installing : python3-setuptools-67.7.2-7.fc40.noarch 49/52 Installing : xz-devel-5.4.4-1.fc39.x86_64 50/52 Installing : bzip2-devel-1.0.8-16.fc39.x86_64 51/52 Installing : zlib-ng-compat-devel-2.1.3-3.fc40.x86_64 52/52 Running scriptlet: zlib-ng-compat-devel-2.1.3-3.fc40.x86_64 52/52 Verifying : glibc-devel-2.38.9000-8.fc40.x86_64 1/52 Verifying : glibc-headers-x86-2.38.9000-8.fc40.noarch 2/52 Verifying : zlib-ng-compat-devel-2.1.3-3.fc40.x86_64 3/52 Verifying : annobin-docs-12.26-1.fc40.noarch 4/52 Verifying : annobin-plugin-gcc-12.26-1.fc40.x86_64 5/52 Verifying : bzip2-devel-1.0.8-16.fc39.x86_64 6/52 Verifying : cpp-13.2.1-1.fc39.x86_64 7/52 Verifying : expat-2.5.0-3.fc39.x86_64 8/52 Verifying : gc-8.2.2-4.fc39.x86_64 9/52 Verifying : gcc-13.2.1-1.fc39.x86_64 10/52 Verifying : gcc-plugin-annobin-13.2.1-1.fc39.x86_64 11/52 Verifying : guile22-2.2.7-9.fc39.x86_64 12/52 Verifying : kernel-headers-6.6.0-0.rc1.git0.1.fc40.x86_64 13/52 Verifying : libb2-0.98.1-9.fc39.x86_64 14/52 Verifying : libmpc-1.3.1-3.fc39.x86_64 15/52 Verifying : libtool-ltdl-2.4.7-8.fc40.x86_64 16/52 Verifying : libxcrypt-devel-4.4.36-2.fc39.x86_64 17/52 Verifying : make-1:4.4.1-2.fc39.x86_64 18/52 Verifying : mpdecimal-2.5.1-7.fc39.x86_64 19/52 Verifying : pyproject-rpm-macros-1.9.0-2.fc39.noarch 20/52 Verifying : python-pip-wheel-23.2.1-1.fc39.noarch 21/52 Verifying : python-rpm-macros-3.12-4.fc40.noarch 22/52 Verifying : python3-3.12.0~rc2-1.fc40.x86_64 23/52 Verifying : python3-babel-2.12.1-4.fc39~bootstrap.noarch 24/52 Verifying : python3-charset-normalizer-3.2.0-2.fc39.noarch 25/52 Verifying : python3-cython-3.0.2-1.fc40.x86_64 26/52 Verifying : python3-devel-3.12.0~rc2-1.fc40.x86_64 27/52 Verifying : python3-docutils-0.20.1-1.fc40.noarch 28/52 Verifying : python3-idna-3.4-5.fc40.noarch 29/52 Verifying : python3-imagesize-1.4.1-5.fc40.noarch 30/52 Verifying : python3-jinja2-3.1.2-6.fc40.noarch 31/52 Verifying : python3-libs-3.12.0~rc2-1.fc40.x86_64 32/52 Verifying : python3-markupsafe-2.1.3-2.fc39.x86_64 33/52 Verifying : python3-packaging-23.1-5.fc40.noarch 34/52 Verifying : python3-pygments-2.16.1-1.fc40.noarch 35/52 Verifying : python3-pysocks-1.7.1-20.fc39.noarch 36/52 Verifying : python3-requests-2.28.2-6.fc40.noarch 37/52 Verifying : python3-rpm-generators-14-7.fc39.noarch 38/52 Verifying : python3-rpm-macros-3.12-4.fc40.noarch 39/52 Verifying : python3-setuptools-67.7.2-7.fc40.noarch 40/52 Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 41/52 Verifying : python3-sphinx-1:7.1.2-1.fc40.noarch 42/52 Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 43/52 Verifying : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 44/52 Verifying : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 45/52 Verifying : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 46/52 Verifying : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 47/52 Verifying : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 48/52 Verifying : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 49/52 Verifying : python3-urllib3+socks-1.26.16-3.fc40.noarch 50/52 Verifying : python3-urllib3-1.26.16-3.fc40.noarch 51/52 Verifying : xz-devel-5.4.4-1.fc39.x86_64 52/52 Installed: annobin-docs-12.26-1.fc40.noarch annobin-plugin-gcc-12.26-1.fc40.x86_64 bzip2-devel-1.0.8-16.fc39.x86_64 cpp-13.2.1-1.fc39.x86_64 expat-2.5.0-3.fc39.x86_64 gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-1.fc39.x86_64 gcc-plugin-annobin-13.2.1-1.fc39.x86_64 glibc-devel-2.38.9000-8.fc40.x86_64 glibc-headers-x86-2.38.9000-8.fc40.noarch guile22-2.2.7-9.fc39.x86_64 kernel-headers-6.6.0-0.rc1.git0.1.fc40.x86_64 libb2-0.98.1-9.fc39.x86_64 libmpc-1.3.1-3.fc39.x86_64 libtool-ltdl-2.4.7-8.fc40.x86_64 libxcrypt-devel-4.4.36-2.fc39.x86_64 make-1:4.4.1-2.fc39.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 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.x86_64 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.x86_64 python3-devel-3.12.0~rc2-1.fc40.x86_64 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.x86_64 python3-markupsafe-2.1.3-2.fc39.x86_64 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.x86_64 zlib-ng-compat-devel-2.1.3-3.fc40.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1693872000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.zxn7O3 + 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.zEnp5w + 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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... yes checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no 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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... yes checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no 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=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-mssse3 -mpopcnt -msse4.1 # pysam: htslib_config HTS_HAVE_NEON= # 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_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/pysam copying pysam/config.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-312/pysam creating build/lib.linux-x86_64-cpython-312/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-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-x86_64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-312/pysam creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/README -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/configure -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/header.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/region.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -mssse3 -mpopcnt -msse4.1 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.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-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o build/temp.linux-x86_64-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_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.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-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-x86_64-cpython-312/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-312/samtools creating build/temp.linux-x86_64-cpython-312/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c: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-x86_64-cpython-312/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.cpython-312-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcutils.o build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcsamtools.cpython-312-x86_64-linux-gnu -lcbcftools.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcutils.cpython-312-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.cpython-312-x86_64-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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-x86_64-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-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-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.21.0/build/lib.linux-x86_64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.21.0/build/lib.linux-x86_64-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.pANvh7 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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.x86_64 --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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... yes checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no 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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... yes checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no 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=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-mssse3 -mpopcnt -msse4.1 # pysam: htslib_config HTS_HAVE_NEON= # 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_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.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.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/ax_check_compile_flag.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/include copying build/lib.linux-x86_64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam byte-compiling /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/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.x86_64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc writing byte-compilation script '/tmp/tmpq1xk8n2e.py' /usr/bin/python3 /tmp/tmpq1xk8n2e.py removing /tmp/tmpq1xk8n2e.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.x86_64/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.x86_64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.21.0-2.fc40 --unique-debug-suffix -0.21.0-2.fc40.x86_64 --unique-debug-src-base python-pysam-0.21.0-2.fc40.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.x86_64 53332 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 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.21.0-2.fc40.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.G3Q9ck + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/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.x86_64/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.x86_64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.sJiCGT + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-312-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-312-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-312-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so()(64bit) libctabix.cpython-312-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-312-x86_64-linux-gnu.so()(64bit) libcutils.cpython-312-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-312-x86_64-linux-gnu.so()(64bit) python-pysam = 0.21.0-2.fc40 python3-pysam = 0.21.0-2.fc40 python3-pysam(x86-64) = 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: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) python(abi) = 3.12 python3.12dist(cython) rtld(GNU_HASH) Obsoletes: python-pysam < 0.21.0-2.fc40 Processing files: python3-pysam-devel-0.21.0-2.fc40.x86_64 Provides: python-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel(x86-64) = 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.mNH7D0 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.21.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.x86_64/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.x86_64/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.x86_64/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.x86_64 Provides: python-pysam-debugsource = 0.21.0-2.fc40 python-pysam-debugsource(x86-64) = 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.x86_64 Provides: debuginfo(build-id) = 038c3fbd4c8d5b25e2ca386dd925abba40afd078 debuginfo(build-id) = 0ad79c687aa966fee6af23bc0cdc7250511b93d3 debuginfo(build-id) = 261643ab9210f39ca238df2e4747060ba50a49b8 debuginfo(build-id) = 2f586b8b36f0908f90df93baef465ded4ecaa0bd debuginfo(build-id) = 318b95a01a6ce6dd71ea42fd2f5efed1a653f097 debuginfo(build-id) = 5b2e130e90454ebb814417c2deb821f321bd0178 debuginfo(build-id) = 780c8c0d46da9fa9740cff19a78b8da48faa3f24 debuginfo(build-id) = 7a534586696548701d07ec594958c053de5b316e debuginfo(build-id) = 7d1d538d52bb2edb57f50b365d671e86b583eb13 debuginfo(build-id) = 8722535756ec2ff828c6c87b3252181f3d969318 debuginfo(build-id) = a1f13ff4bff7585608928e5f59470213eb2709a0 debuginfo(build-id) = c98bbfce2ed099f5b3b14824b9882ce295b4c2d5 debuginfo(build-id) = de7d2057e7696de7b52c5f18365695f27a2006ae libcalignedsegment.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcalignmentfile.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcbcf.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcbgzf.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcfaidx.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcsamfile.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libctabix.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libctabixproxies.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcutils.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) libcvcf.cpython-312-x86_64-linux-gnu.so-0.21.0-2.fc40.x86_64.debug()(64bit) python-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo(x86-64) = 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(x86-64) = 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.x86_64 Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.21.0-2.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.21.0-2.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.21.0-2.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.21.0-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.21.0-2.fc40.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ZVMhYc + 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.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Lin7eF + 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-x86_64-1694963380.989643/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1694963380.989643/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1694963380.989643/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.21.0-2.fc40.src.rpm) Config(child) 7 minutes 2 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "x86_64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "src" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "x86_64" }, { "name": "python3-pysam", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "x86_64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "noarch" } ] } RPMResults finished