Warning: Permanently added '3.84.91.25' (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/6538599-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 0.69 PID: 19736 Logging PID: 19737 Task: {'appstream': False, 'background': False, 'build_id': 6538599, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '4fbad10d375a799758a070a806faa9c4fbda1ce3', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-requests-80586075/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.21.0-2', 'project_dirname': 'python-requests-80586075', 'project_name': 'python-requests-80586075', 'project_owner': 'thrnciar', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/thrnciar/python-requests-80586075/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'thrnciar/python-requests-80586075--thrnciar', 'source_json': {}, 'source_type': None, 'submitter': 'thrnciar', 'tags': [], 'task_id': '6538599-fedora-rawhide-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-requests-80586075/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/python-requests-80586075/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam'... Running: git checkout 4fbad10d375a799758a070a806faa9c4fbda1ce3 -- cmd: ['git', 'checkout', '4fbad10d375a799758a070a806faa9c4fbda1ce3', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam rc: 0 stdout: stderr: Note: switching to '4fbad10d375a799758a070a806faa9c4fbda1ce3'. 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 4fbad10 automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/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 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Downloading pysam-0.21.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o pysam-0.21.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/thrnciar/python-requests-80586075/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 27.2M 0 --:--:-- --:--:-- --:--:-- 27.4M INFO: Reading stdout from command: md5sum pysam-0.21.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1697551560.443277 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1697551560.443277 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam/python-pysam.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.2 INFO: Mock Version: 5.2 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1697551560.443277/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-1697551560.443277/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/efc74c25f3b7f326dc6dda95cacd11f7f14bcd52f291c2e191b36470ebb1f83f/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/efc74c25f3b7f326dc6dda95cacd11f7f14bcd52f291c2e191b36470ebb1f83f/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 77 MB/s | 5.5 MB 00:00 fedora 49 MB/s | 73 MB 00:01 Last metadata expiration check: 0:00:01 ago on Tue Oct 17 14:06:04 2023. Package python3-dnf-4.17.0-6.fc40.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.3-1.fc40 copr_base 302 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc40 fedora 155 k python3-dateutil noarch 1:2.8.2-10.fc40 copr_base 345 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: 3.6 M Downloading Packages: (1/7): dbus-libs-1.14.10-1.fc40.x86_64.rpm 9.9 MB/s | 155 kB 00:00 (2/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 82 MB/s | 157 kB 00:00 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 26 MB/s | 49 kB 00:00 (4/7): python3-six-1.16.0-12.fc39.noarch.rpm 27 MB/s | 41 kB 00:00 (5/7): python3-dnf-plugins-core-4.4.3-1.fc40.no 13 MB/s | 302 kB 00:00 (6/7): python3-systemd-235-5.fc39.x86_64.rpm 45 MB/s | 107 kB 00:00 (7/7): python3-dateutil-2.8.2-10.fc40.noarch.rp 8.4 MB/s | 345 kB 00:00 -------------------------------------------------------------------------------- Total 8.1 MB/s | 1.1 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-10.fc40.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-4.4.3-1.fc40.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.3-1.fc40.noarch 7/7 Verifying : python3-dateutil-1:2.8.2-10.fc40.noarch 1/7 Verifying : python3-dnf-plugins-core-4.4.3-1.fc40.noarch 2/7 Verifying : dbus-libs-1:1.14.10-1.fc40.x86_64 3/7 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 4/7 Verifying : python3-distro-1.8.0-6.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.fc40.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.3-1.fc40.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_64-1697551560.443277/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 83 kB/s | 1.5 kB 00:00 Copr repository 86 MB/s | 5.5 MB 00:00 fedora 794 kB/s | 21 kB 00:00 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 40-0.14 fedora 19 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 2.38.9000-12.fc40 fedora 76 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 269-1.fc40 fedora 81 k rpm-build x86_64 4.19.0-1.fc40 fedora 79 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.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 1.4.3-1.fc40 fedora 149 k authselect-libs x86_64 1.4.3-1.fc40 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.41-7.fc40 fedora 6.3 M binutils-gold x86_64 2.41-7.fc40 fedora 796 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 fedora 863 k coreutils-common x86_64 9.4-1.fc40 fedora 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20230920-1.git570ea89.fc40 fedora 99 k curl x86_64 8.4.0-1.fc40 fedora 362 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 40-0.2 fedora 130 k fedora-release noarch 40-0.14 fedora 8.8 k fedora-release-identity-basic noarch 40-0.14 fedora 9.6 k fedora-repos noarch 40-0.2 fedora 9.3 k fedora-repos-rawhide noarch 40-0.2 fedora 8.9 k file x86_64 5.45-1.fc40 fedora 49 k file-libs x86_64 5.45-1.fc40 fedora 763 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 13.2-11.fc40 fedora 4.2 M gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-3.fc40 fedora 8.1 k glibc x86_64 2.38.9000-12.fc40 fedora 2.2 M glibc-common x86_64 2.38.9000-12.fc40 fedora 358 k glibc-gconv-extra x86_64 2.38.9000-12.fc40 fedora 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.fc40 copr_base 45 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 1.21.2-2.fc40 copr_base 761 k libacl x86_64 2.3.1-10.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 8.4.0-1.fc40 fedora 343 k libdb x86_64 5.3.28-58.fc40 fedora 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 13.2.1-4.fc40 fedora 111 k libgomp x86_64 13.2.1-4.fc40 fedora 320 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 1.57.0-2.fc40 fedora 76 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 13.2.1-4.fc40 fedora 862 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-0.fc40 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 fedora 698 k libzstd x86_64 1.5.5-4.fc39 fedora 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 4.2.1-1.fc40 fedora 343 k ncurses-base noarch 6.4-8.20231001.fc40 fedora 88 k ncurses-libs x86_64 6.4-8.20231001.fc40 fedora 338 k ocaml-srpm-macros noarch 9-1.fc40 fedora 9.0 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 fedora 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 1.10.0-1.fc40 fedora 14 k python-srpm-macros noarch 3.12-4.fc40 fedora 25 k qt5-srpm-macros noarch 5.15.11-1.fc40 fedora 8.3 k qt6-srpm-macros noarch 6.5.3-1.fc40 fedora 8.6 k readline x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.19.0-1.fc40 fedora 538 k rpm-build-libs x86_64 4.19.0-1.fc40 fedora 96 k rpm-libs x86_64 4.19.0-1.fc40 fedora 312 k rpm-sequoia x86_64 1.5.0-1.fc40 fedora 883 k rust-srpm-macros noarch 25.2-2.fc40 fedora 13 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_64 254.5-2.fc40 fedora 688 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 3.0-39.fc40 fedora 266 k zlib x86_64 1.2.13-4.fc39 fedora 94 k zstd x86_64 1.5.5-4.fc39 fedora 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total size: 53 M Installed size: 181 M Downloading Packages: [SKIPPED] jansson-2.13.1-7.fc40.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.21.2-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] alternatives-1.25-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.1.2-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.15-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.41-7.fc40.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.41-7.fc40.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.14-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.11-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20230920-1.git570ea89.fc40.noarch.rpm: Already downloaded [SKIPPED] curl-8.4.0-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-11.fc39.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-10.fc39.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.10-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] ed-1.19-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-9.fc39.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.189-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.189-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.189-6.fc40.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.189-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.189-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-40-0.2.noarch.rpm: Already downloaded [SKIPPED] fedora-release-40-0.14.noarch.rpm: Already downloaded 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[SKIPPED] sqlite-libs-3.43.1-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-254.5-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] tar-1.35-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] unzip-6.0-62.fc39.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.39.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.39.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-40.fc39.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.2-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] xz-5.4.4-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.4.4-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-39.fc40.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.13-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.5-4.fc39.x86_64.rpm: Already downloaded 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. 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cyrus-sasl-lib-2.1.28-11.fc39.x86_64 85/152 Installing : keyutils-libs-1.6.1-7.fc39.x86_64 86/152 Installing : libbrotli-1.1.0-1.fc40.x86_64 87/152 Installing : libdb-5.3.28-58.fc40.x86_64 88/152 Installing : libeconf-0.5.2-1.fc40.x86_64 89/152 Installing : shadow-utils-2:4.14.0-2.fc40.x86_64 90/152 Running scriptlet: libutempter-1.2.1-10.fc39.x86_64 91/152 Installing : libutempter-1.2.1-10.fc39.x86_64 91/152 Installing : libffi-3.4.4-4.fc39.x86_64 92/152 Installing : p11-kit-0.25.0-2.fc39.x86_64 93/152 Installing : libgomp-13.2.1-4.fc40.x86_64 94/152 Installing : libnghttp2-1.57.0-2.fc40.x86_64 95/152 Installing : libpkgconf-1.9.5-2.fc39.x86_64 96/152 Installing : pkgconf-1.9.5-2.fc39.x86_64 97/152 Installing : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 98/152 Installing : libsigsegv-2.14-5.fc39.x86_64 99/152 Installing : gawk-5.2.2-2.fc39.x86_64 100/152 Installing : libtasn1-4.19.0-3.fc39.x86_64 101/152 Installing : p11-kit-trust-0.25.0-2.fc39.x86_64 102/152 Running scriptlet: p11-kit-trust-0.25.0-2.fc39.x86_64 102/152 Installing : libverto-0.3.2-6.fc39.x86_64 103/152 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 104/152 Installing : libssh-config-0.10.5-2.fc39.noarch 105/152 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 106/152 Installing : gnat-srpm-macros-6-3.fc39.noarch 107/152 Installing : ghc-srpm-macros-1.6.1-3.fc40.noarch 108/152 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 109/152 Installing : coreutils-common-9.4-1.fc40.x86_64 110/152 Installing : openssl-libs-1:3.1.1-4.fc40.x86_64 111/152 Installing : coreutils-9.4-1.fc40.x86_64 112/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Installing : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Installing : krb5-libs-1.21.2-2.fc40.x86_64 114/152 Installing : libtirpc-1.3.4-0.fc40.x86_64 115/152 Running scriptlet: authselect-libs-1.4.3-1.fc40.x86_64 116/152 Installing : authselect-libs-1.4.3-1.fc40.x86_64 116/152 Installing : gzip-1.12-6.fc39.x86_64 117/152 Installing : cracklib-2.9.11-2.fc39.x86_64 118/152 Installing : libpwquality-1.4.5-6.fc39.x86_64 119/152 Installing : authselect-1.4.3-1.fc40.x86_64 120/152 Installing : libnsl2-2.0.0-6.fc39.x86_64 121/152 Installing : pam-1.5.3-2.fc39.x86_64 122/152 Installing : libssh-0.10.5-2.fc39.x86_64 123/152 Installing : libarchive-3.7.2-1.fc40.x86_64 124/152 Installing : libevent-2.1.12-9.fc39.x86_64 125/152 Installing : openldap-2.6.6-1.fc39.x86_64 126/152 Installing : libcurl-8.4.0-1.fc40.x86_64 127/152 Installing : elfutils-libs-0.189-6.fc40.x86_64 128/152 Installing : elfutils-debuginfod-client-0.189-6.fc40.x86_64 129/152 Installing : binutils-2.41-7.fc40.x86_64 130/152 Running scriptlet: binutils-2.41-7.fc40.x86_64 130/152 Installing : binutils-gold-2.41-7.fc40.x86_64 131/152 Running scriptlet: binutils-gold-2.41-7.fc40.x86_64 131/152 Installing : elfutils-0.189-6.fc40.x86_64 132/152 Installing : gdb-minimal-13.2-11.fc40.x86_64 133/152 Installing : debugedit-5.0-10.fc39.x86_64 134/152 Installing : curl-8.4.0-1.fc40.x86_64 135/152 Installing : rpm-sequoia-1.5.0-1.fc40.x86_64 136/152 Installing : rpm-libs-4.19.0-1.fc40.x86_64 137/152 Running scriptlet: rpm-4.19.0-1.fc40.x86_64 138/152 Installing : rpm-4.19.0-1.fc40.x86_64 138/152 Installing : efi-srpm-macros-5-9.fc39.noarch 139/152 Installing : lua-srpm-macros-1-9.fc39.noarch 140/152 Installing : rpm-build-libs-4.19.0-1.fc40.x86_64 141/152 Installing : ansible-srpm-macros-1-11.fc39.noarch 142/152 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 143/152 Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 144/152 Installing : go-srpm-macros-3.2.0-7.fc40.noarch 145/152 Installing : python-srpm-macros-3.12-4.fc40.noarch 146/152 Installing : redhat-rpm-config-269-1.fc40.noarch 147/152 Installing : rpm-build-4.19.0-1.fc40.x86_64 148/152 Installing : pyproject-srpm-macros-1.10.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.2-1.fc40.x86_64 150/152 Installing : which-2.21-40.fc39.x86_64 151/152 Installing : info-7.0.3-3.fc39.x86_64 152/152 Running scriptlet: filesystem-3.18-6.fc39.x86_64 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.4.3-1.fc40.x86_64 152/152 Running scriptlet: rpm-4.19.0-1.fc40.x86_64 152/152 Running scriptlet: info-7.0.3-3.fc39.x86_64 152/152 Verifying : jansson-2.13.1-7.fc40.x86_64 1/152 Verifying : krb5-libs-1.21.2-2.fc40.x86_64 2/152 Verifying : alternatives-1.25-1.fc39.x86_64 3/152 Verifying : ansible-srpm-macros-1-11.fc39.noarch 4/152 Verifying : audit-libs-3.1.2-4.fc40.x86_64 5/152 Verifying : authselect-1.4.3-1.fc40.x86_64 6/152 Verifying : authselect-libs-1.4.3-1.fc40.x86_64 7/152 Verifying : basesystem-11-18.fc39.noarch 8/152 Verifying : bash-5.2.15-5.fc39.x86_64 9/152 Verifying : binutils-2.41-7.fc40.x86_64 10/152 Verifying : binutils-gold-2.41-7.fc40.x86_64 11/152 Verifying : bzip2-1.0.8-16.fc39.x86_64 12/152 Verifying : bzip2-libs-1.0.8-16.fc39.x86_64 13/152 Verifying : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 14/152 Verifying : coreutils-9.4-1.fc40.x86_64 15/152 Verifying : coreutils-common-9.4-1.fc40.x86_64 16/152 Verifying : cpio-2.14-4.fc39.x86_64 17/152 Verifying : cracklib-2.9.11-2.fc39.x86_64 18/152 Verifying : crypto-policies-20230920-1.git570ea89.fc40.noarc 19/152 Verifying : curl-8.4.0-1.fc40.x86_64 20/152 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 21/152 Verifying : debugedit-5.0-10.fc39.x86_64 22/152 Verifying : diffutils-3.10-3.fc39.x86_64 23/152 Verifying : dwz-0.15-3.fc39.x86_64 24/152 Verifying : ed-1.19-4.fc39.x86_64 25/152 Verifying : efi-srpm-macros-5-9.fc39.noarch 26/152 Verifying : elfutils-0.189-6.fc40.x86_64 27/152 Verifying : elfutils-debuginfod-client-0.189-6.fc40.x86_64 28/152 Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 29/152 Verifying : elfutils-libelf-0.189-6.fc40.x86_64 30/152 Verifying : elfutils-libs-0.189-6.fc40.x86_64 31/152 Verifying : fedora-gpg-keys-40-0.2.noarch 32/152 Verifying : fedora-release-40-0.14.noarch 33/152 Verifying : fedora-release-common-40-0.14.noarch 34/152 Verifying : fedora-release-identity-basic-40-0.14.noarch 35/152 Verifying : fedora-repos-40-0.2.noarch 36/152 Verifying : fedora-repos-rawhide-40-0.2.noarch 37/152 Verifying : file-5.45-1.fc40.x86_64 38/152 Verifying : file-libs-5.45-1.fc40.x86_64 39/152 Verifying : filesystem-3.18-6.fc39.x86_64 40/152 Verifying : findutils-1:4.9.0-6.fc40.x86_64 41/152 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 42/152 Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 43/152 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 44/152 Verifying : gawk-5.2.2-2.fc39.x86_64 45/152 Verifying : gdb-minimal-13.2-11.fc40.x86_64 46/152 Verifying : gdbm-libs-1:1.23-4.fc39.x86_64 47/152 Verifying : ghc-srpm-macros-1.6.1-3.fc40.noarch 48/152 Verifying : glibc-2.38.9000-12.fc40.x86_64 49/152 Verifying : glibc-common-2.38.9000-12.fc40.x86_64 50/152 Verifying : glibc-gconv-extra-2.38.9000-12.fc40.x86_64 51/152 Verifying : glibc-minimal-langpack-2.38.9000-12.fc40.x86_64 52/152 Verifying : gmp-1:6.2.1-5.fc39.x86_64 53/152 Verifying : gnat-srpm-macros-6-3.fc39.noarch 54/152 Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 55/152 Verifying : grep-3.11-5.fc40.x86_64 56/152 Verifying : gzip-1.12-6.fc39.x86_64 57/152 Verifying : info-7.0.3-3.fc39.x86_64 58/152 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 59/152 Verifying : keyutils-libs-1.6.1-7.fc39.x86_64 60/152 Verifying : libacl-2.3.1-10.fc40.x86_64 61/152 Verifying : libarchive-3.7.2-1.fc40.x86_64 62/152 Verifying : libattr-2.5.1-9.fc40.x86_64 63/152 Verifying : libblkid-2.39.2-1.fc40.x86_64 64/152 Verifying : libbrotli-1.1.0-1.fc40.x86_64 65/152 Verifying : libcap-2.48-7.fc39.x86_64 66/152 Verifying : libcap-ng-0.8.3-8.fc40.x86_64 67/152 Verifying : libcom_err-1.47.0-2.fc39.x86_64 68/152 Verifying : libcurl-8.4.0-1.fc40.x86_64 69/152 Verifying : libdb-5.3.28-58.fc40.x86_64 70/152 Verifying : libeconf-0.5.2-1.fc40.x86_64 71/152 Verifying : libevent-2.1.12-9.fc39.x86_64 72/152 Verifying : libfdisk-2.39.2-1.fc40.x86_64 73/152 Verifying : libffi-3.4.4-4.fc39.x86_64 74/152 Verifying : libgcc-13.2.1-4.fc40.x86_64 75/152 Verifying : libgomp-13.2.1-4.fc40.x86_64 76/152 Verifying : libidn2-2.3.4-3.fc39.x86_64 77/152 Verifying : libmount-2.39.2-1.fc40.x86_64 78/152 Verifying : libnghttp2-1.57.0-2.fc40.x86_64 79/152 Verifying : libnsl2-2.0.0-6.fc39.x86_64 80/152 Verifying : libpkgconf-1.9.5-2.fc39.x86_64 81/152 Verifying : libpsl-0.21.2-4.fc39.x86_64 82/152 Verifying : libpwquality-1.4.5-6.fc39.x86_64 83/152 Verifying : libselinux-3.5-5.fc39.x86_64 84/152 Verifying : libsemanage-3.5-4.fc39.x86_64 85/152 Verifying : libsepol-3.5-2.fc39.x86_64 86/152 Verifying : libsigsegv-2.14-5.fc39.x86_64 87/152 Verifying : libsmartcols-2.39.2-1.fc40.x86_64 88/152 Verifying : libssh-0.10.5-2.fc39.x86_64 89/152 Verifying : libssh-config-0.10.5-2.fc39.noarch 90/152 Verifying : libstdc++-13.2.1-4.fc40.x86_64 91/152 Verifying : libtasn1-4.19.0-3.fc39.x86_64 92/152 Verifying : libtirpc-1.3.4-0.fc40.x86_64 93/152 Verifying : libunistring-1.1-5.fc40.x86_64 94/152 Verifying : libutempter-1.2.1-10.fc39.x86_64 95/152 Verifying : libuuid-2.39.2-1.fc40.x86_64 96/152 Verifying : libverto-0.3.2-6.fc39.x86_64 97/152 Verifying : libxcrypt-4.4.36-2.fc39.x86_64 98/152 Verifying : libxml2-2.11.5-1.fc40.x86_64 99/152 Verifying : libzstd-1.5.5-4.fc39.x86_64 100/152 Verifying : lua-libs-5.4.6-3.fc39.x86_64 101/152 Verifying : lua-srpm-macros-1-9.fc39.noarch 102/152 Verifying : lz4-libs-1.9.4-4.fc39.x86_64 103/152 Verifying : mpfr-4.2.1-1.fc40.x86_64 104/152 Verifying : ncurses-base-6.4-8.20231001.fc40.noarch 105/152 Verifying : ncurses-libs-6.4-8.20231001.fc40.x86_64 106/152 Verifying : ocaml-srpm-macros-9-1.fc40.noarch 107/152 Verifying : openblas-srpm-macros-2-14.fc39.noarch 108/152 Verifying : openldap-2.6.6-1.fc39.x86_64 109/152 Verifying : openssl-libs-1:3.1.1-4.fc40.x86_64 110/152 Verifying : p11-kit-0.25.0-2.fc39.x86_64 111/152 Verifying : p11-kit-trust-0.25.0-2.fc39.x86_64 112/152 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 113/152 Verifying : pam-1.5.3-2.fc39.x86_64 114/152 Verifying : pam-libs-1.5.3-2.fc39.x86_64 115/152 Verifying : patch-2.7.6-22.fc39.x86_64 116/152 Verifying : pcre2-10.42-1.fc39.2.x86_64 117/152 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 118/152 Verifying : perl-srpm-macros-1-51.fc39.noarch 119/152 Verifying : pkgconf-1.9.5-2.fc39.x86_64 120/152 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 121/152 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 122/152 Verifying : popt-1.19-3.fc39.x86_64 123/152 Verifying : publicsuffix-list-dafsa-20230812-1.fc40.noarch 124/152 Verifying : pyproject-srpm-macros-1.10.0-1.fc40.noarch 125/152 Verifying : python-srpm-macros-3.12-4.fc40.noarch 126/152 Verifying : qt5-srpm-macros-5.15.11-1.fc40.noarch 127/152 Verifying : qt6-srpm-macros-6.5.3-1.fc40.noarch 128/152 Verifying : readline-8.2-4.fc39.x86_64 129/152 Verifying : redhat-rpm-config-269-1.fc40.noarch 130/152 Verifying : rpm-4.19.0-1.fc40.x86_64 131/152 Verifying : rpm-build-4.19.0-1.fc40.x86_64 132/152 Verifying : rpm-build-libs-4.19.0-1.fc40.x86_64 133/152 Verifying : rpm-libs-4.19.0-1.fc40.x86_64 134/152 Verifying : rpm-sequoia-1.5.0-1.fc40.x86_64 135/152 Verifying : rust-srpm-macros-25.2-2.fc40.noarch 136/152 Verifying : sed-4.8-14.fc39.x86_64 137/152 Verifying : setup-2.14.4-1.fc39.noarch 138/152 Verifying : shadow-utils-2:4.14.0-2.fc40.x86_64 139/152 Verifying : sqlite-libs-3.43.1-1.fc40.x86_64 140/152 Verifying : systemd-libs-254.5-2.fc40.x86_64 141/152 Verifying : tar-2:1.35-2.fc40.x86_64 142/152 Verifying : unzip-6.0-62.fc39.x86_64 143/152 Verifying : util-linux-2.39.2-1.fc40.x86_64 144/152 Verifying : util-linux-core-2.39.2-1.fc40.x86_64 145/152 Verifying : which-2.21-40.fc39.x86_64 146/152 Verifying : xxhash-libs-0.8.2-1.fc39.x86_64 147/152 Verifying : xz-5.4.4-1.fc39.x86_64 148/152 Verifying : xz-libs-5.4.4-1.fc39.x86_64 149/152 Verifying : zip-3.0-39.fc40.x86_64 150/152 Verifying : zlib-1.2.13-4.fc39.x86_64 151/152 Verifying : zstd-1.5.5-4.fc39.x86_64 152/152 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-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.x86_64 binutils-2.41-7.fc40.x86_64 binutils-gold-2.41-7.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.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.fc39.x86_64 crypto-policies-20230920-1.git570ea89.fc40.noarch curl-8.4.0-1.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-40-0.2.noarch fedora-release-40-0.14.noarch fedora-release-common-40-0.14.noarch fedora-release-identity-basic-40-0.14.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.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-13.2-11.fc40.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-12.fc40.x86_64 glibc-common-2.38.9000-12.fc40.x86_64 glibc-gconv-extra-2.38.9000-12.fc40.x86_64 glibc-minimal-langpack-2.38.9000-12.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.fc40.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-10.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-8.4.0-1.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-13.2.1-4.fc40.x86_64 libgomp-13.2.1-4.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.57.0-2.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++-13.2.1-4.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.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.fc39.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-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.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-1.10.0-1.fc40.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.5.3-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-269-1.fc40.noarch rpm-4.19.0-1.fc40.x86_64 rpm-build-4.19.0-1.fc40.x86_64 rpm-build-libs-4.19.0-1.fc40.x86_64 rpm-libs-4.19.0-1.fc40.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-2.fc40.x86_64 sqlite-libs-3.43.1-1.fc40.x86_64 systemd-libs-254.5-2.fc40.x86_64 tar-2:1.35-2.fc40.x86_64 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-3.0-39.fc40.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.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-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.x86_64 binutils-2.41-7.fc40.x86_64 binutils-gold-2.41-7.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.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.fc39.x86_64 crypto-policies-20230920-1.git570ea89.fc40.noarch curl-8.4.0-1.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-40-0.2.noarch fedora-release-40-0.14.noarch fedora-release-common-40-0.14.noarch fedora-release-identity-basic-40-0.14.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.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-13.2-11.fc40.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-12.fc40.x86_64 glibc-common-2.38.9000-12.fc40.x86_64 glibc-gconv-extra-2.38.9000-12.fc40.x86_64 glibc-minimal-langpack-2.38.9000-12.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.fc40.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-10.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-8.4.0-1.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-13.2.1-4.fc40.x86_64 libgomp-13.2.1-4.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.57.0-2.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++-13.2.1-4.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.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.fc39.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-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.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-1.10.0-1.fc40.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.5.3-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-269-1.fc40.noarch rpm-4.19.0-1.fc40.x86_64 rpm-build-4.19.0-1.fc40.x86_64 rpm-build-libs-4.19.0-1.fc40.x86_64 rpm-libs-4.19.0-1.fc40.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-2.fc40.x86_64 sqlite-libs-3.43.1-1.fc40.x86_64 systemd-libs-254.5-2.fc40.x86_64 tar-1.35-2.fc40.x86_64 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-3.0-39.fc40.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.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_64-1697551560.443277/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1697551560.443277/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1697551560.443277/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-bhyrhwsg/python-pysam/python-pysam.spec) Config(child) 0 minutes 41 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-1697551560.443277/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1697551560.443277/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_64-1697551560.443277/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-4.19.0-1.fc40.x86_64 rpm-sequoia-1.5.0-1.fc40.x86_64 python3-dnf-4.17.0-6.fc40.noarch python3-dnf-plugins-core-4.4.3-1.fc40.noarch yum-4.17.0-6.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 86 kB/s | 1.5 kB 00:00 Copr repository 29 MB/s | 5.5 MB 00:00 fedora 803 kB/s | 21 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 13.2.1-4.fc40 fedora 34 M python3-cython x86_64 3.0.2-1.fc40 fedora 3.8 M python3-devel x86_64 3.12.0-2.fc40 fedora 311 k python3-setuptools noarch 68.2.2-1.fc40 fedora 1.5 M python3-sphinx noarch 1:7.1.2-2.fc40 fedora 2.6 M xz-devel x86_64 5.4.4-1.fc39 fedora 66 k zlib-devel x86_64 1.2.13-4.fc39 fedora 45 k Installing dependencies: annobin-docs noarch 12.28-1.fc40 fedora 94 k annobin-plugin-gcc x86_64 12.28-1.fc40 fedora 959 k cpp x86_64 13.2.1-4.fc40 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 13.2.1-4.fc40 fedora 49 k glibc-devel x86_64 2.38.9000-12.fc40 fedora 91 k glibc-headers-x86 noarch 2.38.9000-12.fc40 fedora 576 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M kernel-headers x86_64 6.6.0-0.rc6.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 1.10.0-1.fc40 fedora 41 k python-pip-wheel noarch 23.2.1-1.fc40 copr_base 1.5 M python-rpm-macros noarch 3.12-4.fc40 fedora 19 k python3 x86_64 3.12.0-2.fc40 fedora 26 k python3-babel noarch 2.12.1-6.fc40 copr_base 6.8 M python3-charset-normalizer noarch 3.3.0-1.fc40 fedora 107 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 copr_base 484 k python3-libs x86_64 3.12.0-2.fc40 fedora 9.2 M python3-markupsafe x86_64 2.1.3-2.fc39 fedora 30 k python3-packaging noarch 23.2-2.fc40 copr_base 116 k python3-pygments noarch 2.16.1-1.fc40 copr_base 2.3 M python3-requests noarch 2.31.0-1.fc40 copr_base 142 k python3-rpm-generators noarch 14-8.fc40 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 1.26.17-2.fc40 fedora 274 k tzdata noarch 2023c-4.fc40 fedora 717 k Transaction Summary ========================================================================================= Install 51 Packages Total size: 88 M Total download size: 2.6 M Installed size: 318 M Downloading Packages: [SKIPPED] python-pip-wheel-23.2.1-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-babel-2.12.1-6.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-jinja2-3.1.2-6.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-packaging-23.2-2.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-requests-2.31.0-1.fc40.noarch.rpm: Already downloaded [SKIPPED] annobin-docs-12.28-1.fc40.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-12.28-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cpp-13.2.1-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] expat-2.5.0-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] gc-8.2.2-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] gcc-13.2.1-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.2.1-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.38.9000-12.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.38.9000-12.fc40.noarch.rpm: Already downloaded [SKIPPED] guile22-2.2.7-9.fc39.x86_64.rpm: Already downloaded [SKIPPED] kernel-headers-6.6.0-0.rc6.git0.1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libb2-0.98.1-9.fc39.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.3.1-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-8.fc40.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.36-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] make-4.4.1-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-7.fc39.x86_64.rpm: Already downloaded [SKIPPED] pyproject-rpm-macros-1.10.0-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python-rpm-macros-3.12-4.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-3.12.0-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] python3-charset-normalizer-3.3.0-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-cython-3.0.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] python3-devel-3.12.0-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] python3-docutils-0.20.1-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-idna-3.4-5.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-imagesize-1.4.1-5.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-libs-3.12.0-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] python3-markupsafe-2.1.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] python3-rpm-generators-14-8.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-macros-3.12-4.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-setuptools-68.2.2-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-snowballstemmer-2.2.0-7.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-sphinx-7.1.2-2.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-sphinx-theme-alabaster-0.7.12-19.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-sphinxcontrib-serializinghtml-1.1.5-10.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-urllib3-1.26.17-2.fc40.noarch.rpm: Already downloaded [SKIPPED] tzdata-2023c-4.fc40.noarch.rpm: Already downloaded (48/51): bzip2-devel-1.0.8-16.fc39.x86_64.rpm 8.6 MB/s | 214 kB 00:00 (49/51): python3-pygments-2.16.1-1.fc40.noarch. 81 MB/s | 2.3 MB 00:00 (50/51): xz-devel-5.4.4-1.fc39.x86_64.rpm 2.3 MB/s | 66 kB 00:00 (51/51): zlib-devel-1.2.13-4.fc39.x86_64.rpm 13 MB/s | 45 kB 00:00 -------------------------------------------------------------------------------- Total 9.5 MB/s | 2.6 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.12-4.fc40.noarch 1/51 Installing : python3-rpm-macros-3.12-4.fc40.noarch 2/51 Installing : libmpc-1.3.1-3.fc39.x86_64 3/51 Installing : cpp-13.2.1-4.fc40.x86_64 4/51 Installing : pyproject-rpm-macros-1.10.0-1.fc40.noarch 5/51 Installing : tzdata-2023c-4.fc40.noarch 6/51 Installing : mpdecimal-2.5.1-7.fc39.x86_64 7/51 Installing : libtool-ltdl-2.4.7-8.fc40.x86_64 8/51 Installing : libb2-0.98.1-9.fc39.x86_64 9/51 Installing : kernel-headers-6.6.0-0.rc6.git0.1.fc40.x86_64 10/51 Installing : glibc-headers-x86-2.38.9000-12.fc40.noarch 11/51 Installing : libxcrypt-devel-4.4.36-2.fc39.x86_64 12/51 Installing : glibc-devel-2.38.9000-12.fc40.x86_64 13/51 Installing : gc-8.2.2-4.fc39.x86_64 14/51 Installing : guile22-2.2.7-9.fc39.x86_64 15/51 Installing : make-1:4.4.1-2.fc39.x86_64 16/51 Installing : gcc-13.2.1-4.fc40.x86_64 17/51 Running scriptlet: gcc-13.2.1-4.fc40.x86_64 17/51 Installing : expat-2.5.0-3.fc39.x86_64 18/51 Installing : annobin-docs-12.28-1.fc40.noarch 19/51 Installing : python-pip-wheel-23.2.1-1.fc40.noarch 20/51 Installing : python3-3.12.0-2.fc40.x86_64 21/51 Installing : python3-libs-3.12.0-2.fc40.x86_64 22/51 Installing : python3-packaging-23.2-2.fc40.noarch 23/51 Installing : python3-idna-3.4-5.fc40.noarch 24/51 Installing : python3-urllib3-1.26.17-2.fc40.noarch 25/51 Installing : python3-rpm-generators-14-8.fc40.noarch 26/51 Installing : python3-babel-2.12.1-6.fc40.noarch 27/51 Installing : python3-pygments-2.16.1-1.fc40.noarch 28/51 Installing : python3-charset-normalizer-3.3.0-1.fc40.noarch 29/51 Installing : python3-requests-2.31.0-1.fc40.noarch 30/51 Installing : python3-docutils-0.20.1-1.fc40.noarch 31/51 Installing : python3-imagesize-1.4.1-5.fc40.noarch 32/51 Installing : python3-markupsafe-2.1.3-2.fc39.x86_64 33/51 Installing : python3-jinja2-3.1.2-6.fc40.noarch 34/51 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 35/51 Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 36/51 Installing : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 37/51 Installing : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 38/51 Installing : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 39/51 Installing : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 40/51 Installing : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 41/51 Installing : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 42/51 Installing : python3-sphinx-1:7.1.2-2.fc40.noarch 43/51 Installing : python3-devel-3.12.0-2.fc40.x86_64 44/51 Installing : python3-cython-3.0.2-1.fc40.x86_64 45/51 Installing : python3-setuptools-68.2.2-1.fc40.noarch 46/51 Installing : annobin-plugin-gcc-12.28-1.fc40.x86_64 47/51 Running scriptlet: annobin-plugin-gcc-12.28-1.fc40.x86_64 47/51 Installing : gcc-plugin-annobin-13.2.1-4.fc40.x86_64 48/51 Running scriptlet: gcc-plugin-annobin-13.2.1-4.fc40.x86_64 48/51 Installing : zlib-devel-1.2.13-4.fc39.x86_64 49/51 Installing : xz-devel-5.4.4-1.fc39.x86_64 50/51 Installing : bzip2-devel-1.0.8-16.fc39.x86_64 51/51 Running scriptlet: bzip2-devel-1.0.8-16.fc39.x86_64 51/51 Verifying : python-pip-wheel-23.2.1-1.fc40.noarch 1/51 Verifying : python3-babel-2.12.1-6.fc40.noarch 2/51 Verifying : python3-jinja2-3.1.2-6.fc40.noarch 3/51 Verifying : python3-packaging-23.2-2.fc40.noarch 4/51 Verifying : python3-pygments-2.16.1-1.fc40.noarch 5/51 Verifying : python3-requests-2.31.0-1.fc40.noarch 6/51 Verifying : annobin-docs-12.28-1.fc40.noarch 7/51 Verifying : annobin-plugin-gcc-12.28-1.fc40.x86_64 8/51 Verifying : bzip2-devel-1.0.8-16.fc39.x86_64 9/51 Verifying : cpp-13.2.1-4.fc40.x86_64 10/51 Verifying : expat-2.5.0-3.fc39.x86_64 11/51 Verifying : gc-8.2.2-4.fc39.x86_64 12/51 Verifying : gcc-13.2.1-4.fc40.x86_64 13/51 Verifying : gcc-plugin-annobin-13.2.1-4.fc40.x86_64 14/51 Verifying : glibc-devel-2.38.9000-12.fc40.x86_64 15/51 Verifying : glibc-headers-x86-2.38.9000-12.fc40.noarch 16/51 Verifying : guile22-2.2.7-9.fc39.x86_64 17/51 Verifying : kernel-headers-6.6.0-0.rc6.git0.1.fc40.x86_64 18/51 Verifying : libb2-0.98.1-9.fc39.x86_64 19/51 Verifying : libmpc-1.3.1-3.fc39.x86_64 20/51 Verifying : libtool-ltdl-2.4.7-8.fc40.x86_64 21/51 Verifying : libxcrypt-devel-4.4.36-2.fc39.x86_64 22/51 Verifying : make-1:4.4.1-2.fc39.x86_64 23/51 Verifying : mpdecimal-2.5.1-7.fc39.x86_64 24/51 Verifying : pyproject-rpm-macros-1.10.0-1.fc40.noarch 25/51 Verifying : python-rpm-macros-3.12-4.fc40.noarch 26/51 Verifying : python3-3.12.0-2.fc40.x86_64 27/51 Verifying : python3-charset-normalizer-3.3.0-1.fc40.noarch 28/51 Verifying : python3-cython-3.0.2-1.fc40.x86_64 29/51 Verifying : python3-devel-3.12.0-2.fc40.x86_64 30/51 Verifying : python3-docutils-0.20.1-1.fc40.noarch 31/51 Verifying : python3-idna-3.4-5.fc40.noarch 32/51 Verifying : python3-imagesize-1.4.1-5.fc40.noarch 33/51 Verifying : python3-libs-3.12.0-2.fc40.x86_64 34/51 Verifying : python3-markupsafe-2.1.3-2.fc39.x86_64 35/51 Verifying : python3-rpm-generators-14-8.fc40.noarch 36/51 Verifying : python3-rpm-macros-3.12-4.fc40.noarch 37/51 Verifying : python3-setuptools-68.2.2-1.fc40.noarch 38/51 Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 39/51 Verifying : python3-sphinx-1:7.1.2-2.fc40.noarch 40/51 Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 41/51 Verifying : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 42/51 Verifying : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 43/51 Verifying : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 44/51 Verifying : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 45/51 Verifying : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 46/51 Verifying : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 47/51 Verifying : python3-urllib3-1.26.17-2.fc40.noarch 48/51 Verifying : tzdata-2023c-4.fc40.noarch 49/51 Verifying : xz-devel-5.4.4-1.fc39.x86_64 50/51 Verifying : zlib-devel-1.2.13-4.fc39.x86_64 51/51 Installed: annobin-docs-12.28-1.fc40.noarch annobin-plugin-gcc-12.28-1.fc40.x86_64 bzip2-devel-1.0.8-16.fc39.x86_64 cpp-13.2.1-4.fc40.x86_64 expat-2.5.0-3.fc39.x86_64 gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-4.fc40.x86_64 gcc-plugin-annobin-13.2.1-4.fc40.x86_64 glibc-devel-2.38.9000-12.fc40.x86_64 glibc-headers-x86-2.38.9000-12.fc40.noarch guile22-2.2.7-9.fc39.x86_64 kernel-headers-6.6.0-0.rc6.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-1.10.0-1.fc40.noarch python-pip-wheel-23.2.1-1.fc40.noarch python-rpm-macros-3.12-4.fc40.noarch python3-3.12.0-2.fc40.x86_64 python3-babel-2.12.1-6.fc40.noarch python3-charset-normalizer-3.3.0-1.fc40.noarch python3-cython-3.0.2-1.fc40.x86_64 python3-devel-3.12.0-2.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-3.12.0-2.fc40.x86_64 python3-markupsafe-2.1.3-2.fc39.x86_64 python3-packaging-23.2-2.fc40.noarch python3-pygments-2.16.1-1.fc40.noarch python3-requests-2.31.0-1.fc40.noarch python3-rpm-generators-14-8.fc40.noarch python3-rpm-macros-3.12-4.fc40.noarch python3-setuptools-68.2.2-1.fc40.noarch python3-snowballstemmer-2.2.0-7.fc39.noarch python3-sphinx-1:7.1.2-2.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-urllib3-1.26.17-2.fc40.noarch tzdata-2023c-4.fc40.noarch xz-devel-5.4.4-1.fc39.x86_64 zlib-devel-1.2.13-4.fc39.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.KGZa6I + 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.dJSGhi + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Cstrip=none -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 library containing regcomp... configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support 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:204: _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:204: _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:204: _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:204: _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:204: _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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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.NGVLNL + 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Cstrip=none -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 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/tmpiq_igifv.py' /usr/bin/python3 /tmp/tmpiq_igifv.py removing /tmp/tmpiq_igifv.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.UU40Qi + 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.lJn7Ye + 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.bZmb0C + 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) = 092b8f2f300d65a31df4973e32c4f422a2ad1a7c debuginfo(build-id) = 0b92ab0259735a9b28e937d96a5cd153470db4d3 debuginfo(build-id) = 117b5afc3d090e99e2e6a93914378d2b804d1bce debuginfo(build-id) = 14e9b8c2006109b2ca1b214162dc895bb0c5a185 debuginfo(build-id) = 375c8ceeb5c09dfe7e1ff8613e1105ea28ce0507 debuginfo(build-id) = 3c8a06e0ba512cdbb022480e6ee843500486f3cb debuginfo(build-id) = 4cac489750bb0c995f35293cf394a37465b71f57 debuginfo(build-id) = 6eb9b710b421b7c3a2e2dd3b6aefb3f823f54ca8 debuginfo(build-id) = 7556b5951c1907a998dae389763d9cc4abd663c2 debuginfo(build-id) = 8fe38ab041726ef308fc01d47edd56f8535e1607 debuginfo(build-id) = c4899d767318d046cfeafd98b7645ca96e8c3629 debuginfo(build-id) = edd04d2809bf02ec02be3e2885cd5b3c614667b7 debuginfo(build-id) = f72e454c58c2c34899f70d7915d0ceb17885833d 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/python3-pysam-debuginfo-0.21.0-2.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-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.6Ggm0p + 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.TEsCgI + 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_64-1697551560.443277/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1697551560.443277/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1697551560.443277/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.21.0-2.fc40.src.rpm) Config(child) 6 minutes 39 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python3-pysam-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": "python3-pysam-debuginfo", "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" }, { "name": "python-pysam", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "src" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.21.0", "release": "2.fc40", "arch": "x86_64" } ] } RPMResults finished