Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c149' (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/7625619-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.73 PID: 6475 Logging PID: 6476 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 7625619, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '1f2b16ed759a2f27447ffa2ddd6dcbf3e6bc8db2', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/setuptools-impact-check-control/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.22.1-1', 'project_dirname': 'setuptools-impact-check-control', 'project_name': 'setuptools-impact-check-control', 'project_owner': 'thrnciar', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/thrnciar/setuptools-impact-check-control/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'thrnciar/setuptools-impact-check-control--https://src.fedoraproject.org/user/davidsch', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'https://src.fedoraproject.org/user/davidsch', 'tags': [], 'task_id': '7625619-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/thrnciar/setuptools-impact-check-control/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/setuptools-impact-check-control/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam'... Running: git checkout 1f2b16ed759a2f27447ffa2ddd6dcbf3e6bc8db2 -- cmd: ['git', 'checkout', '1f2b16ed759a2f27447ffa2ddd6dcbf3e6bc8db2', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam rc: 0 stdout: stderr: Note: switching to '1f2b16ed759a2f27447ffa2ddd6dcbf3e6bc8db2'. 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 1f2b16e automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading pysam-0.22.1.tar.gz INFO: Calling: curl -H Pragma: -o pysam-0.22.1.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/thrnciar/setuptools-impact-check-control/python-pysam/pysam-0.22.1.tar.gz/md5/1ad924c322e8acaa946c2a8ed1366a82/pysam-0.22.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4534k 100 4534k 0 0 37.6M 0 --:--:-- --:--:-- --:--:-- 37.8M INFO: Reading stdout from command: md5sum pysam-0.22.1.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1718739368.112563 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1718739368.112563 -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-umesxpz1/python-pysam/python-pysam.spec) Config(fedora-39-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1718739368.112563/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:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1718739368.112563/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/53bae686d2e2bedd23bab671ad33de8ca99f38839206149edbdf4dea17efe99a/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/53bae686d2e2bedd23bab671ad33de8ca99f38839206149edbdf4dea17efe99a/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 14 MB/s | 2.0 MB 00:00 fedora 26 MB/s | 89 MB 00:03 updates 4.6 MB/s | 38 MB 00:08 Last metadata expiration check: 0:00:01 ago on Tue Jun 18 19:36:39 2024. Package python3-dnf-4.19.2-1.fc39.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.6.0-1.fc39 updates 317 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc39 fedora 156 k python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k python3-dbus x86_64 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd x86_64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.2 M Installed size: 3.6 M Downloading Packages: (1/7): dbus-libs-1.14.10-1.fc39.x86_64.rpm 276 kB/s | 156 kB 00:00 (2/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 264 kB/s | 157 kB 00:00 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 602 kB/s | 49 kB 00:00 (4/7): python3-six-1.16.0-12.fc39.noarch.rpm 546 kB/s | 41 kB 00:00 (5/7): python3-systemd-235-5.fc39.x86_64.rpm 658 kB/s | 107 kB 00:00 (6/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 397 kB/s | 355 kB 00:00 (7/7): python3-dnf-plugins-core-4.6.0-1.fc39.no 662 kB/s | 317 kB 00:00 -------------------------------------------------------------------------------- Total 980 kB/s | 1.2 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc39.x86_64 5/7 Installing : python3-dbus-1.3.2-4.fc39.x86_64 6/7 Installing : python3-dnf-plugins-core-4.6.0-1.fc39.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.6.0-1.fc39.noarch 7/7 Verifying : dbus-libs-1:1.14.10-1.fc39.x86_64 1/7 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 3/7 Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7 Verifying : python3-six-1.16.0-12.fc39.noarch 5/7 Verifying : python3-systemd-235-5.fc39.x86_64 6/7 Verifying : python3-dnf-plugins-core-4.6.0-1.fc39.noarch 7/7 Installed: dbus-libs-1:1.14.10-1.fc39.x86_64 python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1718739368.112563/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) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-3.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 15 MB/s | 2.0 MB 00:00 fedora 39 MB/s | 89 MB 00:02 updates 28 MB/s | 38 MB 00:01 Last metadata expiration check: 0:00:01 ago on Tue Jun 18 19:37:24 2024. Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.26-1.fc39 updates 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.3-5.fc39 updates 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 39-36 updates 19 k findutils x86_64 1:4.9.0-5.fc39 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38-18.fc39 updates 73 k grep x86_64 3.11-3.fc39 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 266-1.fc39 updates 78 k rpm-build x86_64 4.19.1.1-1.fc39 updates 78 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.fc39 updates 1.3 M tar x86_64 2:1.35-2.fc39 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.4-1.fc39 updates 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 1.26-1.fc39 updates 39 k ansible-srpm-macros noarch 1-12.fc39 updates 21 k audit-libs x86_64 3.1.3-1.fc39 updates 124 k authselect x86_64 1.4.3-1.fc39 fedora 149 k authselect-libs x86_64 1.4.3-1.fc39 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.40-14.fc39 updates 5.6 M binutils-gold x86_64 2.40-14.fc39 updates 795 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-2.fc39 fedora 837 k coreutils-common x86_64 9.3-5.fc39 updates 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20231204-1.git1e3a2e4.fc39 updates 100 k curl x86_64 8.2.1-5.fc39 updates 344 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-12.fc39 updates 79 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 0.191-2.fc39 updates 559 k elfutils-debuginfod-client x86_64 0.191-2.fc39 updates 38 k elfutils-default-yama-scope noarch 0.191-2.fc39 updates 13 k elfutils-libelf x86_64 0.191-2.fc39 updates 209 k elfutils-libs x86_64 0.191-2.fc39 updates 263 k fedora-gpg-keys noarch 39-2 updates 130 k fedora-release noarch 39-36 updates 8.6 k fedora-release-identity-basic noarch 39-36 updates 9.4 k fedora-repos noarch 39-2 updates 9.3 k file x86_64 5.44-5.fc39 fedora 49 k file-libs x86_64 5.44-5.fc39 fedora 729 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 0.3.1-1.fc39 updates 19 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal x86_64 14.2-1.fc39 updates 4.3 M gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc x86_64 2.38-18.fc39 updates 2.2 M glibc-common x86_64 2.38-18.fc39 updates 353 k glibc-gconv-extra x86_64 2.38-18.fc39 updates 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 3.5.0-1.fc39 updates 28 k jansson x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.3-1.fc39 updates 31 k krb5-libs x86_64 1.21.2-3.fc39 updates 765 k libacl x86_64 2.3.1-9.fc39 updates 23 k libarchive x86_64 3.7.1-2.fc39 updates 407 k libattr x86_64 2.5.1-8.fc39 fedora 18 k libblkid x86_64 2.39.4-1.fc39 updates 116 k libbrotli x86_64 1.1.0-1.fc39 fedora 336 k libcap x86_64 2.48-9.fc39 updates 68 k libcap-ng x86_64 0.8.3-8.fc39 fedora 32 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.2.1-5.fc39 updates 322 k libdb x86_64 5.3.28-56.fc39 fedora 760 k libeconf x86_64 0.5.2-2.fc39 updates 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.4-1.fc39 updates 161 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.3.1-1.fc39 updates 118 k libgomp x86_64 13.3.1-1.fc39 updates 328 k libidn2 x86_64 2.3.7-1.fc39 updates 119 k libmount x86_64 2.39.4-1.fc39 updates 154 k libnghttp2 x86_64 1.55.1-5.fc39 updates 75 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-6.fc39 fedora 120 k libselinux x86_64 3.5-5.fc39 fedora 87 k libsemanage x86_64 3.5-4.fc39 fedora 120 k libsepol x86_64 3.5-2.fc39 fedora 324 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.4-1.fc39 updates 67 k libssh x86_64 0.10.6-2.fc39 updates 212 k libssh-config noarch 0.10.6-2.fc39 updates 9.0 k libstdc++ x86_64 13.3.1-1.fc39 updates 869 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-1.rc3.fc39 updates 93 k libtool-ltdl x86_64 2.4.7-7.fc39 fedora 36 k libunistring x86_64 1.1-5.fc39 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.4-1.fc39 updates 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 2.10.4-3.fc39 fedora 701 k libzstd x86_64 1.5.6-1.fc39 updates 312 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-13.fc39 updates 8.7 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.0-3.fc39 fedora 344 k ncurses-base noarch 6.4-7.20230520.fc39.1 updates 88 k ncurses-libs x86_64 6.4-7.20230520.fc39.1 updates 336 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.7-1.fc39 updates 254 k openssl-libs x86_64 1:3.1.1-4.fc39 fedora 2.2 M p11-kit x86_64 0.25.3-1.fc39 updates 520 k p11-kit-trust x86_64 0.25.3-1.fc39 updates 140 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-3.fc39 updates 542 k pam-libs x86_64 1.5.3-3.fc39 updates 56 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 20240107-1.fc39 updates 58 k pyproject-srpm-macros noarch 1.12.0-1.fc39 updates 14 k python-srpm-macros noarch 3.12-4.fc39 fedora 25 k qt5-srpm-macros noarch 5.15.13-1.fc39 updates 8.5 k qt6-srpm-macros noarch 6.6.2-1.fc39 updates 8.9 k readline x86_64 8.2-6.fc39 updates 212 k rpm x86_64 4.19.1.1-1.fc39 updates 538 k rpm-build-libs x86_64 4.19.1.1-1.fc39 updates 95 k rpm-libs x86_64 4.19.1.1-1.fc39 updates 312 k rpm-sequoia x86_64 1.6.0-3.fc39 updates 847 k rpmautospec-rpm-macros noarch 0.6.3-1.fc39 updates 10 k rust-srpm-macros noarch 26.3-1.fc39 updates 13 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs x86_64 3.42.0-7.fc39 fedora 678 k systemd-libs x86_64 254.13-1.fc39 updates 684 k util-linux-core x86_64 2.39.4-1.fc39 updates 507 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.fc39 fedora 266 k zlib x86_64 1.2.13-4.fc39 fedora 94 k zstd x86_64 1.5.6-1.fc39 updates 479 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 153 Packages Total download size: 52 M Installed size: 179 M Downloading Packages: (1/153): basesystem-11-18.fc39.noarch.rpm 24 kB/s | 7.2 kB 00:00 (2/153): bzip2-1.0.8-16.fc39.x86_64.rpm 690 kB/s | 52 kB 00:00 (3/153): authselect-1.4.3-1.fc39.x86_64.rpm 365 kB/s | 149 kB 00:00 (4/153): bzip2-libs-1.0.8-16.fc39.x86_64.rpm 938 kB/s | 41 kB 00:00 (5/153): authselect-libs-1.4.3-1.fc39.x86_64.rp 569 kB/s | 249 kB 00:00 (6/153): cracklib-2.9.11-2.fc39.x86_64.rpm 2.5 MB/s | 94 kB 00:00 (7/153): ca-certificates-2023.2.60_v7.0.306-2.f 6.8 MB/s | 837 kB 00:00 (8/153): cpio-2.14-4.fc39.x86_64.rpm 2.6 MB/s | 279 kB 00:00 (9/153): cyrus-sasl-lib-2.1.28-11.fc39.x86_64.r 8.5 MB/s | 793 kB 00:00 (10/153): dwz-0.15-3.fc39.x86_64.rpm 3.5 MB/s | 134 kB 00:00 (11/153): diffutils-3.10-3.fc39.x86_64.rpm 8.7 MB/s | 398 kB 00:00 (12/153): ed-1.19-4.fc39.x86_64.rpm 2.5 MB/s | 79 kB 00:00 (13/153): efi-srpm-macros-5-9.fc39.noarch.rpm 736 kB/s | 22 kB 00:00 (14/153): file-5.44-5.fc39.x86_64.rpm 1.6 MB/s | 49 kB 00:00 (15/153): findutils-4.9.0-5.fc39.x86_64.rpm 12 MB/s | 492 kB 00:00 (16/153): file-libs-5.44-5.fc39.x86_64.rpm 15 MB/s | 729 kB 00:00 (17/153): fonts-srpm-macros-2.0.5-12.fc39.noarc 916 kB/s | 26 kB 00:00 (18/153): fpc-srpm-macros-1.3-8.fc39.noarch.rpm 252 kB/s | 7.4 kB 00:00 (19/153): filesystem-3.18-6.fc39.x86_64.rpm 12 MB/s | 1.1 MB 00:00 (20/153): gdbm-libs-1.23-4.fc39.x86_64.rpm 1.8 MB/s | 56 kB 00:00 (21/153): ghc-srpm-macros-1.6.1-2.fc39.noarch.r 261 kB/s | 7.8 kB 00:00 (22/153): gawk-5.2.2-2.fc39.x86_64.rpm 20 MB/s | 1.1 MB 00:00 (23/153): gmp-6.2.1-5.fc39.x86_64.rpm 8.4 MB/s | 313 kB 00:00 (24/153): gnat-srpm-macros-6-3.fc39.noarch.rpm 300 kB/s | 8.8 kB 00:00 (25/153): grep-3.11-3.fc39.x86_64.rpm 8.6 MB/s | 298 kB 00:00 (26/153): gzip-1.12-6.fc39.x86_64.rpm 5.0 MB/s | 166 kB 00:00 (27/153): info-7.0.3-3.fc39.x86_64.rpm 5.5 MB/s | 182 kB 00:00 (28/153): jansson-2.13.1-7.fc39.x86_64.rpm 1.5 MB/s | 44 kB 00:00 (29/153): kernel-srpm-macros-1.0-20.fc39.noarch 356 kB/s | 10 kB 00:00 (30/153): libattr-2.5.1-8.fc39.x86_64.rpm 594 kB/s | 18 kB 00:00 (31/153): libbrotli-1.1.0-1.fc39.x86_64.rpm 9.4 MB/s | 336 kB 00:00 (32/153): libcap-ng-0.8.3-8.fc39.x86_64.rpm 1.1 MB/s | 32 kB 00:00 (33/153): libcom_err-1.47.0-2.fc39.x86_64.rpm 878 kB/s | 26 kB 00:00 (34/153): libdb-5.3.28-56.fc39.x86_64.rpm 18 MB/s | 760 kB 00:00 (35/153): libevent-2.1.12-9.fc39.x86_64.rpm 7.2 MB/s | 258 kB 00:00 (36/153): libffi-3.4.4-4.fc39.x86_64.rpm 1.3 MB/s | 40 kB 00:00 (37/153): libpkgconf-1.9.5-2.fc39.x86_64.rpm 1.2 MB/s | 38 kB 00:00 (38/153): libpsl-0.21.2-4.fc39.x86_64.rpm 2.0 MB/s | 63 kB 00:00 (39/153): libnsl2-2.0.0-6.fc39.x86_64.rpm 503 kB/s | 30 kB 00:00 (40/153): libpwquality-1.4.5-6.fc39.x86_64.rpm 3.7 MB/s | 120 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tar-1.35-2.fc39.x86_64.rpm 21 MB/s | 864 kB 00:00 (71/153): sqlite-libs-3.42.0-7.fc39.x86_64.rpm 15 MB/s | 678 kB 00:00 (72/153): which-2.21-40.fc39.x86_64.rpm 1.4 MB/s | 42 kB 00:00 (73/153): xxhash-libs-0.8.2-1.fc39.x86_64.rpm 1.2 MB/s | 37 kB 00:00 (74/153): unzip-6.0-62.fc39.x86_64.rpm 4.1 MB/s | 184 kB 00:00 (75/153): xz-libs-5.4.4-1.fc39.x86_64.rpm 3.4 MB/s | 108 kB 00:00 (76/153): xz-5.4.4-1.fc39.x86_64.rpm 13 MB/s | 556 kB 00:00 (77/153): zip-3.0-39.fc39.x86_64.rpm 7.5 MB/s | 266 kB 00:00 (78/153): zlib-1.2.13-4.fc39.x86_64.rpm 3.0 MB/s | 94 kB 00:00 (79/153): ansible-srpm-macros-1-12.fc39.noarch. 68 kB/s | 21 kB 00:00 (80/153): alternatives-1.26-1.fc39.x86_64.rpm 113 kB/s | 39 kB 00:00 (81/153): audit-libs-3.1.3-1.fc39.x86_64.rpm 277 kB/s | 124 kB 00:00 (82/153): binutils-gold-2.40-14.fc39.x86_64.rpm 2.3 MB/s | 795 kB 00:00 (83/153): bash-5.2.26-1.fc39.x86_64.rpm 2.9 MB/s | 1.8 MB 00:00 (84/153): coreutils-9.3-5.fc39.x86_64.rpm 6.3 MB/s | 1.1 MB 00:00 (85/153): binutils-2.40-14.fc39.x86_64.rpm 7.8 MB/s | 5.6 MB 00:00 (86/153): crypto-policies-20231204-1.git1e3a2e4 1.0 MB/s | 100 kB 00:00 (87/153): coreutils-common-9.3-5.fc39.x86_64.rp 13 MB/s | 2.1 MB 00:00 (88/153): curl-8.2.1-5.fc39.x86_64.rpm 4.0 MB/s | 344 kB 00:00 (89/153): elfutils-0.191-2.fc39.x86_64.rpm 6.2 MB/s | 559 kB 00:00 (90/153): debugedit-5.0-12.fc39.x86_64.rpm 655 kB/s | 79 kB 00:00 (91/153): elfutils-debuginfod-client-0.191-2.fc 476 kB/s | 38 kB 00:00 (92/153): elfutils-default-yama-scope-0.191-2.f 165 kB/s | 13 kB 00:00 (93/153): elfutils-libs-0.191-2.fc39.x86_64.rpm 3.1 MB/s | 263 kB 00:00 (94/153): elfutils-libelf-0.191-2.fc39.x86_64.r 1.6 MB/s | 209 kB 00:00 (95/153): fedora-gpg-keys-39-2.noarch.rpm 1.5 MB/s | 130 kB 00:00 (96/153): fedora-release-common-39-36.noarch.rp 176 kB/s | 19 kB 00:00 (97/153): fedora-repos-39-2.noarch.rpm 73 kB/s | 9.3 kB 00:00 (98/153): forge-srpm-macros-0.3.1-1.fc39.noarch 242 kB/s | 19 kB 00:00 (99/153): fedora-release-39-36.noarch.rpm 19 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libgcc-13.3.1-1.fc39.x86_64.rpm 937 kB/s | 118 kB 00:00 (115/153): libfdisk-2.39.4-1.fc39.x86_64.rpm 1.2 MB/s | 161 kB 00:00 (116/153): libidn2-2.3.7-1.fc39.x86_64.rpm 1.4 MB/s | 119 kB 00:00 (117/153): libgomp-13.3.1-1.fc39.x86_64.rpm 3.7 MB/s | 328 kB 00:00 (118/153): gdb-minimal-14.2-1.fc39.x86_64.rpm 2.6 MB/s | 4.3 MB 00:01 (119/153): libnghttp2-1.55.1-5.fc39.x86_64.rpm 879 kB/s | 75 kB 00:00 (120/153): libmount-2.39.4-1.fc39.x86_64.rpm 1.7 MB/s | 154 kB 00:00 (121/153): libsmartcols-2.39.4-1.fc39.x86_64.rp 460 kB/s | 67 kB 00:00 (122/153): libstdc++-13.3.1-1.fc39.x86_64.rpm 6.0 MB/s | 869 kB 00:00 (123/153): libtirpc-1.3.4-1.rc3.fc39.x86_64.rpm 858 kB/s | 93 kB 00:00 (124/153): libssh-0.10.6-2.fc39.x86_64.rpm 524 kB/s | 212 kB 00:00 (125/153): libssh-config-0.10.6-2.fc39.noarch.r 22 kB/s | 9.0 kB 00:00 (126/153): libuuid-2.39.4-1.fc39.x86_64.rpm 347 kB/s | 28 kB 00:00 (127/153): libzstd-1.5.6-1.fc39.x86_64.rpm 3.6 MB/s | 312 kB 00:00 (128/153): lua-srpm-macros-1-13.fc39.noarch.rpm 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(143/153): rpm-4.19.1.1-1.fc39.x86_64.rpm 4.8 MB/s | 538 kB 00:00 (144/153): rpm-build-4.19.1.1-1.fc39.x86_64.rpm 635 kB/s | 78 kB 00:00 (145/153): rpm-libs-4.19.1.1-1.fc39.x86_64.rpm 3.4 MB/s | 312 kB 00:00 (146/153): rpmautospec-rpm-macros-0.6.3-1.fc39. 77 kB/s | 10 kB 00:00 (147/153): rust-srpm-macros-26.3-1.fc39.noarch. 157 kB/s | 13 kB 00:00 (148/153): rpm-sequoia-1.6.0-3.fc39.x86_64.rpm 4.5 MB/s | 847 kB 00:00 (149/153): util-linux-2.39.4-1.fc39.x86_64.rpm 8.3 MB/s | 1.2 MB 00:00 (150/153): systemd-libs-254.13-1.fc39.x86_64.rp 3.1 MB/s | 684 kB 00:00 (151/153): shadow-utils-4.14.0-2.fc39.x86_64.rp 5.5 MB/s | 1.3 MB 00:00 (152/153): util-linux-core-2.39.4-1.fc39.x86_64 3.4 MB/s | 507 kB 00:00 (153/153): zstd-1.5.6-1.fc39.x86_64.rpm 3.0 MB/s | 479 kB 00:00 -------------------------------------------------------------------------------- Total 7.8 MB/s | 52 MB 00:06 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.3.1-1.fc39.x86_64 1/153 Running scriptlet: libgcc-13.3.1-1.fc39.x86_64 1/153 Installing : crypto-policies-20231204-1.git1e3a2e4.fc39.noarc 2/153 Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc39.noarc 2/153 Installing : fedora-release-identity-basic-39-36.noarch 3/153 Installing : fedora-gpg-keys-39-2.noarch 4/153 Installing : fedora-repos-39-2.noarch 5/153 Installing : fedora-release-common-39-36.noarch 6/153 Installing : fedora-release-39-36.noarch 7/153 Installing : setup-2.14.4-1.fc39.noarch 8/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.4-1.fc39.noarch 8/153 Installing : filesystem-3.18-6.fc39.x86_64 9/153 Installing : basesystem-11-18.fc39.noarch 10/153 Installing : rust-srpm-macros-26.3-1.fc39.noarch 11/153 Installing : qt6-srpm-macros-6.6.2-1.fc39.noarch 12/153 Installing : qt5-srpm-macros-5.15.13-1.fc39.noarch 13/153 Installing : publicsuffix-list-dafsa-20240107-1.fc39.noarch 14/153 Installing : ncurses-base-6.4-7.20230520.fc39.1.noarch 15/153 Installing : glibc-gconv-extra-2.38-18.fc39.x86_64 16/153 Running scriptlet: glibc-gconv-extra-2.38-18.fc39.x86_64 16/153 Installing : glibc-minimal-langpack-2.38-18.fc39.x86_64 17/153 Installing : glibc-common-2.38-18.fc39.x86_64 18/153 Running scriptlet: glibc-2.38-18.fc39.x86_64 19/153 Installing : glibc-2.38-18.fc39.x86_64 19/153 Running scriptlet: glibc-2.38-18.fc39.x86_64 19/153 Installing : ncurses-libs-6.4-7.20230520.fc39.1.x86_64 20/153 Installing : bash-5.2.26-1.fc39.x86_64 21/153 Running scriptlet: bash-5.2.26-1.fc39.x86_64 21/153 Installing : zlib-1.2.13-4.fc39.x86_64 22/153 Installing : xz-libs-5.4.4-1.fc39.x86_64 23/153 Installing : bzip2-libs-1.0.8-16.fc39.x86_64 24/153 Installing : popt-1.19-3.fc39.x86_64 25/153 Installing : libstdc++-13.3.1-1.fc39.x86_64 26/153 Installing : libuuid-2.39.4-1.fc39.x86_64 27/153 Installing : libzstd-1.5.6-1.fc39.x86_64 28/153 Installing : elfutils-libelf-0.191-2.fc39.x86_64 29/153 Installing : libblkid-2.39.4-1.fc39.x86_64 30/153 Installing : readline-8.2-6.fc39.x86_64 31/153 Installing : gmp-1:6.2.1-5.fc39.x86_64 32/153 Installing : libattr-2.5.1-8.fc39.x86_64 33/153 Installing : libacl-2.3.1-9.fc39.x86_64 34/153 Installing : libxcrypt-4.4.36-2.fc39.x86_64 35/153 Installing : libcap-2.48-9.fc39.x86_64 36/153 Installing : lz4-libs-1.9.4-4.fc39.x86_64 37/153 Installing : libeconf-0.5.2-2.fc39.x86_64 38/153 Installing : systemd-libs-254.13-1.fc39.x86_64 39/153 Installing : mpfr-4.2.0-3.fc39.x86_64 40/153 Installing : dwz-0.15-3.fc39.x86_64 41/153 Installing : unzip-6.0-62.fc39.x86_64 42/153 Installing : file-libs-5.44-5.fc39.x86_64 43/153 Installing : file-5.44-5.fc39.x86_64 44/153 Installing : jansson-2.13.1-7.fc39.x86_64 45/153 Installing : libcap-ng-0.8.3-8.fc39.x86_64 46/153 Installing : audit-libs-3.1.3-1.fc39.x86_64 47/153 Installing : pam-libs-1.5.3-3.fc39.x86_64 48/153 Installing : libcom_err-1.47.0-2.fc39.x86_64 49/153 Installing : libsepol-3.5-2.fc39.x86_64 50/153 Installing : libtasn1-4.19.0-3.fc39.x86_64 51/153 Installing : libunistring-1.1-5.fc39.x86_64 52/153 Installing : libidn2-2.3.7-1.fc39.x86_64 53/153 Installing : lua-libs-5.4.6-3.fc39.x86_64 54/153 Installing : alternatives-1.26-1.fc39.x86_64 55/153 Installing : libsmartcols-2.39.4-1.fc39.x86_64 56/153 Installing : libpsl-0.21.2-4.fc39.x86_64 57/153 Installing : zip-3.0-39.fc39.x86_64 58/153 Installing : zstd-1.5.6-1.fc39.x86_64 59/153 Installing : libfdisk-2.39.4-1.fc39.x86_64 60/153 Installing : bzip2-1.0.8-16.fc39.x86_64 61/153 Installing : libxml2-2.10.4-3.fc39.x86_64 62/153 Installing : sqlite-libs-3.42.0-7.fc39.x86_64 63/153 Installing : ed-1.19-4.fc39.x86_64 64/153 Installing : elfutils-default-yama-scope-0.191-2.fc39.noarch 65/153 Running scriptlet: elfutils-default-yama-scope-0.191-2.fc39.noarch 65/153 Installing : cpio-2.14-4.fc39.x86_64 66/153 Installing : diffutils-3.10-3.fc39.x86_64 67/153 Installing : gdbm-libs-1:1.23-4.fc39.x86_64 68/153 Installing : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 69/153 Installing : libbrotli-1.1.0-1.fc39.x86_64 70/153 Installing : libdb-5.3.28-56.fc39.x86_64 71/153 Installing : libffi-3.4.4-4.fc39.x86_64 72/153 Installing : p11-kit-0.25.3-1.fc39.x86_64 73/153 Installing : p11-kit-trust-0.25.3-1.fc39.x86_64 74/153 Running scriptlet: p11-kit-trust-0.25.3-1.fc39.x86_64 74/153 Installing : libpkgconf-1.9.5-2.fc39.x86_64 75/153 Installing : pkgconf-1.9.5-2.fc39.x86_64 76/153 Installing : libsigsegv-2.14-5.fc39.x86_64 77/153 Installing : gawk-5.2.2-2.fc39.x86_64 78/153 Installing : libtool-ltdl-2.4.7-7.fc39.x86_64 79/153 Installing : libverto-0.3.2-6.fc39.x86_64 80/153 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 81/153 Installing : keyutils-libs-1.6.3-1.fc39.x86_64 82/153 Installing : libgomp-13.3.1-1.fc39.x86_64 83/153 Installing : libnghttp2-1.55.1-5.fc39.x86_64 84/153 Installing : libssh-config-0.10.6-2.fc39.noarch 85/153 Installing : coreutils-common-9.3-5.fc39.x86_64 86/153 Installing : ansible-srpm-macros-1-12.fc39.noarch 87/153 Installing : pkgconf-m4-1.9.5-2.fc39.noarch 88/153 Installing : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 89/153 Installing : perl-srpm-macros-1-51.fc39.noarch 90/153 Installing : pcre2-syntax-10.42-1.fc39.2.noarch 91/153 Installing : pcre2-10.42-1.fc39.2.x86_64 92/153 Installing : libselinux-3.5-5.fc39.x86_64 93/153 Installing : sed-4.8-14.fc39.x86_64 94/153 Installing : grep-3.11-3.fc39.x86_64 95/153 Installing : findutils-1:4.9.0-5.fc39.x86_64 96/153 Installing : xz-5.4.4-1.fc39.x86_64 97/153 Installing : libmount-2.39.4-1.fc39.x86_64 98/153 Installing : util-linux-core-2.39.4-1.fc39.x86_64 99/153 Installing : openssl-libs-1:3.1.1-4.fc39.x86_64 100/153 Installing : coreutils-9.3-5.fc39.x86_64 101/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 102/153 Installing : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 102/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 102/153 Installing : krb5-libs-1.21.2-3.fc39.x86_64 103/153 Installing : libtirpc-1.3.4-1.rc3.fc39.x86_64 104/153 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 105/153 Installing : authselect-libs-1.4.3-1.fc39.x86_64 105/153 Installing : gzip-1.12-6.fc39.x86_64 106/153 Installing : libarchive-3.7.1-2.fc39.x86_64 107/153 Installing : cracklib-2.9.11-2.fc39.x86_64 108/153 Installing : libpwquality-1.4.5-6.fc39.x86_64 109/153 Installing : authselect-1.4.3-1.fc39.x86_64 110/153 Installing : libnsl2-2.0.0-6.fc39.x86_64 111/153 Installing : pam-1.5.3-3.fc39.x86_64 112/153 Installing : libssh-0.10.6-2.fc39.x86_64 113/153 Installing : libevent-2.1.12-9.fc39.x86_64 114/153 Installing : openldap-2.6.7-1.fc39.x86_64 115/153 Installing : libcurl-8.2.1-5.fc39.x86_64 116/153 Installing : elfutils-libs-0.191-2.fc39.x86_64 117/153 Installing : elfutils-debuginfod-client-0.191-2.fc39.x86_64 118/153 Installing : binutils-gold-2.40-14.fc39.x86_64 119/153 Running scriptlet: binutils-gold-2.40-14.fc39.x86_64 119/153 Installing : binutils-2.40-14.fc39.x86_64 120/153 Running scriptlet: binutils-2.40-14.fc39.x86_64 120/153 Installing : elfutils-0.191-2.fc39.x86_64 121/153 Installing : gdb-minimal-14.2-1.fc39.x86_64 122/153 Installing : debugedit-5.0-12.fc39.x86_64 123/153 Installing : curl-8.2.1-5.fc39.x86_64 124/153 Installing : rpm-sequoia-1.6.0-3.fc39.x86_64 125/153 Installing : rpm-libs-4.19.1.1-1.fc39.x86_64 126/153 Running scriptlet: rpm-4.19.1.1-1.fc39.x86_64 127/153 Installing : rpm-4.19.1.1-1.fc39.x86_64 127/153 Installing : efi-srpm-macros-5-9.fc39.noarch 128/153 Installing : lua-srpm-macros-1-13.fc39.noarch 129/153 Installing : rpmautospec-rpm-macros-0.6.3-1.fc39.noarch 130/153 Installing : rpm-build-libs-4.19.1.1-1.fc39.x86_64 131/153 Installing : libsemanage-3.5-4.fc39.x86_64 132/153 Installing : shadow-utils-2:4.14.0-2.fc39.x86_64 133/153 Running scriptlet: libutempter-1.2.1-10.fc39.x86_64 134/153 Installing : libutempter-1.2.1-10.fc39.x86_64 134/153 Installing : patch-2.7.6-22.fc39.x86_64 135/153 Installing : tar-2:1.35-2.fc39.x86_64 136/153 Installing : package-notes-srpm-macros-0.5-9.fc39.noarch 137/153 Installing : openblas-srpm-macros-2-14.fc39.noarch 138/153 Installing : ocaml-srpm-macros-8-2.fc39.noarch 139/153 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 140/153 Installing : gnat-srpm-macros-6-3.fc39.noarch 141/153 Installing : ghc-srpm-macros-1.6.1-2.fc39.noarch 142/153 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 143/153 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 144/153 Installing : python-srpm-macros-3.12-4.fc39.noarch 145/153 Installing : forge-srpm-macros-0.3.1-1.fc39.noarch 146/153 Installing : go-srpm-macros-3.5.0-1.fc39.noarch 147/153 Installing : redhat-rpm-config-266-1.fc39.noarch 148/153 Installing : rpm-build-4.19.1.1-1.fc39.x86_64 149/153 Installing : pyproject-srpm-macros-1.12.0-1.fc39.noarch 150/153 Installing : util-linux-2.39.4-1.fc39.x86_64 151/153 Running scriptlet: util-linux-2.39.4-1.fc39.x86_64 151/153 Installing : which-2.21-40.fc39.x86_64 152/153 Installing : info-7.0.3-3.fc39.x86_64 153/153 Running scriptlet: filesystem-3.18-6.fc39.x86_64 153/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 153/153 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 153/153 Running scriptlet: rpm-4.19.1.1-1.fc39.x86_64 153/153 Running scriptlet: info-7.0.3-3.fc39.x86_64 153/153 Verifying : authselect-1.4.3-1.fc39.x86_64 1/153 Verifying : authselect-libs-1.4.3-1.fc39.x86_64 2/153 Verifying : basesystem-11-18.fc39.noarch 3/153 Verifying : bzip2-1.0.8-16.fc39.x86_64 4/153 Verifying : bzip2-libs-1.0.8-16.fc39.x86_64 5/153 Verifying : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 6/153 Verifying : cpio-2.14-4.fc39.x86_64 7/153 Verifying : cracklib-2.9.11-2.fc39.x86_64 8/153 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 9/153 Verifying : diffutils-3.10-3.fc39.x86_64 10/153 Verifying : dwz-0.15-3.fc39.x86_64 11/153 Verifying : ed-1.19-4.fc39.x86_64 12/153 Verifying : efi-srpm-macros-5-9.fc39.noarch 13/153 Verifying : file-5.44-5.fc39.x86_64 14/153 Verifying : file-libs-5.44-5.fc39.x86_64 15/153 Verifying : filesystem-3.18-6.fc39.x86_64 16/153 Verifying : findutils-1:4.9.0-5.fc39.x86_64 17/153 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 18/153 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 19/153 Verifying : gawk-5.2.2-2.fc39.x86_64 20/153 Verifying : gdbm-libs-1:1.23-4.fc39.x86_64 21/153 Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 22/153 Verifying : gmp-1:6.2.1-5.fc39.x86_64 23/153 Verifying : gnat-srpm-macros-6-3.fc39.noarch 24/153 Verifying : grep-3.11-3.fc39.x86_64 25/153 Verifying : gzip-1.12-6.fc39.x86_64 26/153 Verifying : info-7.0.3-3.fc39.x86_64 27/153 Verifying : jansson-2.13.1-7.fc39.x86_64 28/153 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 29/153 Verifying : libattr-2.5.1-8.fc39.x86_64 30/153 Verifying : libbrotli-1.1.0-1.fc39.x86_64 31/153 Verifying : libcap-ng-0.8.3-8.fc39.x86_64 32/153 Verifying : libcom_err-1.47.0-2.fc39.x86_64 33/153 Verifying : libdb-5.3.28-56.fc39.x86_64 34/153 Verifying : libevent-2.1.12-9.fc39.x86_64 35/153 Verifying : libffi-3.4.4-4.fc39.x86_64 36/153 Verifying : libnsl2-2.0.0-6.fc39.x86_64 37/153 Verifying : libpkgconf-1.9.5-2.fc39.x86_64 38/153 Verifying : libpsl-0.21.2-4.fc39.x86_64 39/153 Verifying : libpwquality-1.4.5-6.fc39.x86_64 40/153 Verifying : libselinux-3.5-5.fc39.x86_64 41/153 Verifying : libsemanage-3.5-4.fc39.x86_64 42/153 Verifying : libsepol-3.5-2.fc39.x86_64 43/153 Verifying : libsigsegv-2.14-5.fc39.x86_64 44/153 Verifying : libtasn1-4.19.0-3.fc39.x86_64 45/153 Verifying : libtool-ltdl-2.4.7-7.fc39.x86_64 46/153 Verifying : libunistring-1.1-5.fc39.x86_64 47/153 Verifying : libutempter-1.2.1-10.fc39.x86_64 48/153 Verifying : libverto-0.3.2-6.fc39.x86_64 49/153 Verifying : libxcrypt-4.4.36-2.fc39.x86_64 50/153 Verifying : libxml2-2.10.4-3.fc39.x86_64 51/153 Verifying : lua-libs-5.4.6-3.fc39.x86_64 52/153 Verifying : lz4-libs-1.9.4-4.fc39.x86_64 53/153 Verifying : mpfr-4.2.0-3.fc39.x86_64 54/153 Verifying : ocaml-srpm-macros-8-2.fc39.noarch 55/153 Verifying : openblas-srpm-macros-2-14.fc39.noarch 56/153 Verifying : openssl-libs-1:3.1.1-4.fc39.x86_64 57/153 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 58/153 Verifying : patch-2.7.6-22.fc39.x86_64 59/153 Verifying : pcre2-10.42-1.fc39.2.x86_64 60/153 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 61/153 Verifying : perl-srpm-macros-1-51.fc39.noarch 62/153 Verifying : pkgconf-1.9.5-2.fc39.x86_64 63/153 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 64/153 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 65/153 Verifying : popt-1.19-3.fc39.x86_64 66/153 Verifying : python-srpm-macros-3.12-4.fc39.noarch 67/153 Verifying : sed-4.8-14.fc39.x86_64 68/153 Verifying : setup-2.14.4-1.fc39.noarch 69/153 Verifying : sqlite-libs-3.42.0-7.fc39.x86_64 70/153 Verifying : tar-2:1.35-2.fc39.x86_64 71/153 Verifying : unzip-6.0-62.fc39.x86_64 72/153 Verifying : which-2.21-40.fc39.x86_64 73/153 Verifying : xxhash-libs-0.8.2-1.fc39.x86_64 74/153 Verifying : xz-5.4.4-1.fc39.x86_64 75/153 Verifying : xz-libs-5.4.4-1.fc39.x86_64 76/153 Verifying : zip-3.0-39.fc39.x86_64 77/153 Verifying : zlib-1.2.13-4.fc39.x86_64 78/153 Verifying : alternatives-1.26-1.fc39.x86_64 79/153 Verifying : ansible-srpm-macros-1-12.fc39.noarch 80/153 Verifying : audit-libs-3.1.3-1.fc39.x86_64 81/153 Verifying : bash-5.2.26-1.fc39.x86_64 82/153 Verifying : binutils-2.40-14.fc39.x86_64 83/153 Verifying : binutils-gold-2.40-14.fc39.x86_64 84/153 Verifying : coreutils-9.3-5.fc39.x86_64 85/153 Verifying : coreutils-common-9.3-5.fc39.x86_64 86/153 Verifying : crypto-policies-20231204-1.git1e3a2e4.fc39.noarc 87/153 Verifying : curl-8.2.1-5.fc39.x86_64 88/153 Verifying : debugedit-5.0-12.fc39.x86_64 89/153 Verifying : elfutils-0.191-2.fc39.x86_64 90/153 Verifying : elfutils-debuginfod-client-0.191-2.fc39.x86_64 91/153 Verifying : elfutils-default-yama-scope-0.191-2.fc39.noarch 92/153 Verifying : elfutils-libelf-0.191-2.fc39.x86_64 93/153 Verifying : elfutils-libs-0.191-2.fc39.x86_64 94/153 Verifying : fedora-gpg-keys-39-2.noarch 95/153 Verifying : fedora-release-39-36.noarch 96/153 Verifying : fedora-release-common-39-36.noarch 97/153 Verifying : fedora-release-identity-basic-39-36.noarch 98/153 Verifying : fedora-repos-39-2.noarch 99/153 Verifying : forge-srpm-macros-0.3.1-1.fc39.noarch 100/153 Verifying : gdb-minimal-14.2-1.fc39.x86_64 101/153 Verifying : glibc-2.38-18.fc39.x86_64 102/153 Verifying : glibc-common-2.38-18.fc39.x86_64 103/153 Verifying : glibc-gconv-extra-2.38-18.fc39.x86_64 104/153 Verifying : glibc-minimal-langpack-2.38-18.fc39.x86_64 105/153 Verifying : go-srpm-macros-3.5.0-1.fc39.noarch 106/153 Verifying : keyutils-libs-1.6.3-1.fc39.x86_64 107/153 Verifying : krb5-libs-1.21.2-3.fc39.x86_64 108/153 Verifying : libacl-2.3.1-9.fc39.x86_64 109/153 Verifying : libarchive-3.7.1-2.fc39.x86_64 110/153 Verifying : libblkid-2.39.4-1.fc39.x86_64 111/153 Verifying : libcap-2.48-9.fc39.x86_64 112/153 Verifying : libcurl-8.2.1-5.fc39.x86_64 113/153 Verifying : libeconf-0.5.2-2.fc39.x86_64 114/153 Verifying : libfdisk-2.39.4-1.fc39.x86_64 115/153 Verifying : libgcc-13.3.1-1.fc39.x86_64 116/153 Verifying : libgomp-13.3.1-1.fc39.x86_64 117/153 Verifying : libidn2-2.3.7-1.fc39.x86_64 118/153 Verifying : libmount-2.39.4-1.fc39.x86_64 119/153 Verifying : libnghttp2-1.55.1-5.fc39.x86_64 120/153 Verifying : libsmartcols-2.39.4-1.fc39.x86_64 121/153 Verifying : libssh-0.10.6-2.fc39.x86_64 122/153 Verifying : libssh-config-0.10.6-2.fc39.noarch 123/153 Verifying : libstdc++-13.3.1-1.fc39.x86_64 124/153 Verifying : libtirpc-1.3.4-1.rc3.fc39.x86_64 125/153 Verifying : libuuid-2.39.4-1.fc39.x86_64 126/153 Verifying : libzstd-1.5.6-1.fc39.x86_64 127/153 Verifying : lua-srpm-macros-1-13.fc39.noarch 128/153 Verifying : ncurses-base-6.4-7.20230520.fc39.1.noarch 129/153 Verifying : ncurses-libs-6.4-7.20230520.fc39.1.x86_64 130/153 Verifying : openldap-2.6.7-1.fc39.x86_64 131/153 Verifying : p11-kit-0.25.3-1.fc39.x86_64 132/153 Verifying : p11-kit-trust-0.25.3-1.fc39.x86_64 133/153 Verifying : pam-1.5.3-3.fc39.x86_64 134/153 Verifying : pam-libs-1.5.3-3.fc39.x86_64 135/153 Verifying : publicsuffix-list-dafsa-20240107-1.fc39.noarch 136/153 Verifying : pyproject-srpm-macros-1.12.0-1.fc39.noarch 137/153 Verifying : qt5-srpm-macros-5.15.13-1.fc39.noarch 138/153 Verifying : qt6-srpm-macros-6.6.2-1.fc39.noarch 139/153 Verifying : readline-8.2-6.fc39.x86_64 140/153 Verifying : redhat-rpm-config-266-1.fc39.noarch 141/153 Verifying : rpm-4.19.1.1-1.fc39.x86_64 142/153 Verifying : rpm-build-4.19.1.1-1.fc39.x86_64 143/153 Verifying : rpm-build-libs-4.19.1.1-1.fc39.x86_64 144/153 Verifying : rpm-libs-4.19.1.1-1.fc39.x86_64 145/153 Verifying : rpm-sequoia-1.6.0-3.fc39.x86_64 146/153 Verifying : rpmautospec-rpm-macros-0.6.3-1.fc39.noarch 147/153 Verifying : rust-srpm-macros-26.3-1.fc39.noarch 148/153 Verifying : shadow-utils-2:4.14.0-2.fc39.x86_64 149/153 Verifying : systemd-libs-254.13-1.fc39.x86_64 150/153 Verifying : util-linux-2.39.4-1.fc39.x86_64 151/153 Verifying : util-linux-core-2.39.4-1.fc39.x86_64 152/153 Verifying : zstd-1.5.6-1.fc39.x86_64 153/153 Installed: alternatives-1.26-1.fc39.x86_64 ansible-srpm-macros-1-12.fc39.noarch audit-libs-3.1.3-1.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.26-1.fc39.x86_64 binutils-2.40-14.fc39.x86_64 binutils-gold-2.40-14.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-5.fc39.x86_64 coreutils-common-9.3-5.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc39.noarch curl-8.2.1-5.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.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-0.191-2.fc39.x86_64 elfutils-debuginfod-client-0.191-2.fc39.x86_64 elfutils-default-yama-scope-0.191-2.fc39.noarch elfutils-libelf-0.191-2.fc39.x86_64 elfutils-libs-0.191-2.fc39.x86_64 fedora-gpg-keys-39-2.noarch fedora-release-39-36.noarch fedora-release-common-39-36.noarch fedora-release-identity-basic-39-36.noarch fedora-repos-39-2.noarch file-5.44-5.fc39.x86_64 file-libs-5.44-5.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-5.fc39.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.3.1-1.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.2-1.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-18.fc39.x86_64 glibc-common-2.38-18.fc39.x86_64 glibc-gconv-extra-2.38-18.fc39.x86_64 glibc-minimal-langpack-2.38-18.fc39.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.5.0-1.fc39.noarch grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc39.x86_64 krb5-libs-1.21.2-3.fc39.x86_64 libacl-2.3.1-9.fc39.x86_64 libarchive-3.7.1-2.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.4-1.fc39.x86_64 libbrotli-1.1.0-1.fc39.x86_64 libcap-2.48-9.fc39.x86_64 libcap-ng-0.8.3-8.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-5.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-2.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.4-1.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.3.1-1.fc39.x86_64 libgomp-13.3.1-1.fc39.x86_64 libidn2-2.3.7-1.fc39.x86_64 libmount-2.39.4-1.fc39.x86_64 libnghttp2-1.55.1-5.fc39.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-2.39.4-1.fc39.x86_64 libssh-0.10.6-2.fc39.x86_64 libssh-config-0.10.6-2.fc39.noarch libstdc++-13.3.1-1.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-1.rc3.fc39.x86_64 libtool-ltdl-2.4.7-7.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.4-1.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.10.4-3.fc39.x86_64 libzstd-1.5.6-1.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-13.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.1.noarch ncurses-libs-6.4-7.20230520.fc39.1.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.7-1.fc39.x86_64 openssl-libs-1:3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.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-20240107-1.fc39.noarch pyproject-srpm-macros-1.12.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.13-1.fc39.noarch qt6-srpm-macros-6.6.2-1.fc39.noarch readline-8.2-6.fc39.x86_64 redhat-rpm-config-266-1.fc39.noarch rpm-4.19.1.1-1.fc39.x86_64 rpm-build-4.19.1.1-1.fc39.x86_64 rpm-build-libs-4.19.1.1-1.fc39.x86_64 rpm-libs-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-3.fc39.x86_64 rpmautospec-rpm-macros-0.6.3-1.fc39.noarch rust-srpm-macros-26.3-1.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.13-1.fc39.x86_64 tar-2:1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.4-1.fc39.x86_64 util-linux-core-2.39.4-1.fc39.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.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.6-1.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-1.26-1.fc39.x86_64 ansible-srpm-macros-1-12.fc39.noarch audit-libs-3.1.3-1.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.26-1.fc39.x86_64 binutils-2.40-14.fc39.x86_64 binutils-gold-2.40-14.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-5.fc39.x86_64 coreutils-common-9.3-5.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc39.noarch curl-8.2.1-5.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.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-0.191-2.fc39.x86_64 elfutils-debuginfod-client-0.191-2.fc39.x86_64 elfutils-default-yama-scope-0.191-2.fc39.noarch elfutils-libelf-0.191-2.fc39.x86_64 elfutils-libs-0.191-2.fc39.x86_64 fedora-gpg-keys-39-2.noarch fedora-release-39-36.noarch fedora-release-common-39-36.noarch fedora-release-identity-basic-39-36.noarch fedora-repos-39-2.noarch file-5.44-5.fc39.x86_64 file-libs-5.44-5.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-5.fc39.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.3.1-1.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.2-1.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-18.fc39.x86_64 glibc-common-2.38-18.fc39.x86_64 glibc-gconv-extra-2.38-18.fc39.x86_64 glibc-minimal-langpack-2.38-18.fc39.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.5.0-1.fc39.noarch gpg-pubkey-18b8e74c-62f2920f grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc39.x86_64 krb5-libs-1.21.2-3.fc39.x86_64 libacl-2.3.1-9.fc39.x86_64 libarchive-3.7.1-2.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.4-1.fc39.x86_64 libbrotli-1.1.0-1.fc39.x86_64 libcap-2.48-9.fc39.x86_64 libcap-ng-0.8.3-8.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-5.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-2.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.4-1.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.3.1-1.fc39.x86_64 libgomp-13.3.1-1.fc39.x86_64 libidn2-2.3.7-1.fc39.x86_64 libmount-2.39.4-1.fc39.x86_64 libnghttp2-1.55.1-5.fc39.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-2.39.4-1.fc39.x86_64 libssh-0.10.6-2.fc39.x86_64 libssh-config-0.10.6-2.fc39.noarch libstdc++-13.3.1-1.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-1.rc3.fc39.x86_64 libtool-ltdl-2.4.7-7.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.4-1.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.10.4-3.fc39.x86_64 libzstd-1.5.6-1.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-13.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.1.noarch ncurses-libs-6.4-7.20230520.fc39.1.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.7-1.fc39.x86_64 openssl-libs-3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.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-20240107-1.fc39.noarch pyproject-srpm-macros-1.12.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.13-1.fc39.noarch qt6-srpm-macros-6.6.2-1.fc39.noarch readline-8.2-6.fc39.x86_64 redhat-rpm-config-266-1.fc39.noarch rpm-4.19.1.1-1.fc39.x86_64 rpm-build-4.19.1.1-1.fc39.x86_64 rpm-build-libs-4.19.1.1-1.fc39.x86_64 rpm-libs-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-3.fc39.x86_64 rpmautospec-rpm-macros-0.6.3-1.fc39.noarch rust-srpm-macros-26.3-1.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.13-1.fc39.x86_64 tar-1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.4-1.fc39.x86_64 util-linux-core-2.39.4-1.fc39.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.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.6-1.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1718323200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.1-1.fc39.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.log /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.rpm.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-umesxpz1/python-pysam/python-pysam.spec) Config(child) 1 minutes 46 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/python-pysam-0.22.1-1.fc39.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1718739368.112563/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1718739368.112563/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-39-x86_64-1718739368.112563/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-3.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch Finish: chroot init Start: build phase for python-pysam-0.22.1-1.fc39.src.rpm Start: build setup for python-pysam-0.22.1-1.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1718323200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.1-1.fc39.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 45 kB/s | 1.5 kB 00:00 fedora 1.2 MB/s | 32 kB 00:00 updates 1.1 MB/s | 27 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 13.3.1-1.fc39 updates 34 M python3-cython x86_64 3.0.6-1.fc39 updates 3.8 M python3-devel x86_64 3.12.3-2.fc39 updates 313 k python3-setuptools noarch 67.7.2-7.fc39 fedora 1.5 M python3-sphinx noarch 1:7.2.6-8.fc39 copr_base 2.5 M python3-sphinx_rtd_theme noarch 1.2.2-1.fc39 fedora 84 k 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 12.51-1.fc39 updates 88 k annobin-plugin-gcc x86_64 12.51-1.fc39 updates 959 k cpp x86_64 13.3.1-1.fc39 updates 11 M expat x86_64 2.6.2-1.fc39 updates 114 k fontawesome4-fonts noarch 1:4.7.0-19.fc39 fedora 204 k fonts-filesystem noarch 1:2.0.5-12.fc39 fedora 8.2 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc-plugin-annobin x86_64 13.3.1-1.fc39 updates 56 k glibc-devel x86_64 2.38-18.fc39 updates 86 k glibc-headers-x86 noarch 2.38-18.fc39 updates 571 k google-roboto-slab-fonts noarch 1.100263-0.21.20150923git.fc39 fedora 239 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M kernel-headers x86_64 6.9.4-100.fc39 updates 1.6 M lato-fonts noarch 2.015-17.fc39 fedora 3.1 M libb2 x86_64 0.98.1-9.fc39 fedora 25 k libmpc x86_64 1.3.1-3.fc39 fedora 70 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 1.12.0-1.fc39 updates 41 k python-pip-wheel noarch 23.2.1-2.fc39 updates 1.5 M python-rpm-macros noarch 3.12-4.fc39 fedora 19 k python3 x86_64 3.12.3-2.fc39 updates 27 k python3-babel noarch 2.12.1-6.fc39 fedora 6.9 M python3-charset-normalizer noarch 3.2.0-2.fc39 fedora 105 k python3-docutils noarch 0.19-5.fc39 fedora 1.0 M python3-idna noarch 3.7-1.fc39 updates 116 k python3-imagesize noarch 1.4.1-4.fc39 fedora 22 k python3-jinja2 noarch 3.1.4-1.fc39 updates 485 k python3-libs x86_64 3.12.3-2.fc39 updates 9.2 M python3-markupsafe x86_64 2.1.3-2.fc39 fedora 30 k python3-packaging noarch 23.1-4.fc39 fedora 114 k python3-pygments noarch 2.15.1-4.fc39 fedora 2.4 M python3-pysocks noarch 1.7.1-20.fc39 fedora 39 k python3-requests noarch 2.28.2-5.fc39 fedora 152 k python3-rpm-generators noarch 14-7.fc39 fedora 30 k python3-rpm-macros noarch 3.12-4.fc39 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-jquery noarch 4.1-3.fc39 fedora 113 k python3-urllib3 noarch 1.26.18-1.fc39 updates 274 k python3-urllib3+socks noarch 1.26.18-1.fc39 updates 10 k tzdata noarch 2024a-2.fc39 updates 715 k Transaction Summary ========================================================================================= Install 52 Packages Total download size: 91 M Installed size: 331 M Downloading Packages: (1/52): python3-sphinx-7.2.6-8.fc39.noarch.rpm 25 MB/s | 2.5 MB 00:00 (2/52): fonts-filesystem-2.0.5-12.fc39.noarch.r 46 kB/s | 8.2 kB 00:00 (3/52): fontawesome4-fonts-4.7.0-19.fc39.noarch 421 kB/s | 204 kB 00:00 (4/52): bzip2-devel-1.0.8-16.fc39.x86_64.rpm 409 kB/s | 214 kB 00:00 (5/52): google-roboto-slab-fonts-1.100263-0.21. 1.4 MB/s | 239 kB 00:00 (6/52): gc-8.2.2-4.fc39.x86_64.rpm 281 kB/s | 110 kB 00:00 (7/52): libb2-0.98.1-9.fc39.x86_64.rpm 248 kB/s | 25 kB 00:00 (8/52): libmpc-1.3.1-3.fc39.x86_64.rpm 517 kB/s | 70 kB 00:00 (9/52): libxcrypt-devel-4.4.36-2.fc39.x86_64.rp 283 kB/s | 30 kB 00:00 (10/52): lato-fonts-2.015-17.fc39.noarch.rpm 8.4 MB/s | 3.1 MB 00:00 (11/52): guile22-2.2.7-9.fc39.x86_64.rpm 11 MB/s | 6.5 MB 00:00 (12/52): mpdecimal-2.5.1-7.fc39.x86_64.rpm 1.1 MB/s | 89 kB 00:00 (13/52): python-rpm-macros-3.12-4.fc39.noarch.r 230 kB/s | 19 kB 00:00 (14/52): make-4.4.1-2.fc39.x86_64.rpm 1.9 MB/s | 589 kB 00:00 (15/52): python3-charset-normalizer-3.2.0-2.fc3 660 kB/s | 105 kB 00:00 (16/52): python3-imagesize-1.4.1-4.fc39.noarch. 153 kB/s | 22 kB 00:00 (17/52): python3-babel-2.12.1-6.fc39.noarch.rpm 16 MB/s | 6.9 MB 00:00 (18/52): python3-docutils-0.19-5.fc39.noarch.rp 4.8 MB/s | 1.0 MB 00:00 (19/52): python3-markupsafe-2.1.3-2.fc39.x86_64 342 kB/s | 30 kB 00:00 (20/52): python3-packaging-23.1-4.fc39.noarch.r 1.3 MB/s | 114 kB 00:00 (21/52): python3-pysocks-1.7.1-20.fc39.noarch.r 458 kB/s | 39 kB 00:00 (22/52): python3-requests-2.28.2-5.fc39.noarch. 1.9 MB/s | 152 kB 00:00 (23/52): python3-rpm-generators-14-7.fc39.noarc 336 kB/s | 30 kB 00:00 (24/52): python3-pygments-2.15.1-4.fc39.noarch. 11 MB/s | 2.4 MB 00:00 (25/52): python3-rpm-macros-3.12-4.fc39.noarch. 169 kB/s | 14 kB 00:00 (26/52): python3-setuptools-67.7.2-7.fc39.noarc 14 MB/s | 1.5 MB 00:00 (27/52): python3-sphinx-theme-alabaster-0.7.12- 346 kB/s | 29 kB 00:00 (28/52): python3-snowballstemmer-2.2.0-7.fc39.n 2.0 MB/s | 257 kB 00:00 (29/52): python3-sphinx_rtd_theme-1.2.2-1.fc39. 937 kB/s | 84 kB 00:00 (30/52): python3-sphinxcontrib-jquery-4.1-3.fc3 1.1 MB/s | 113 kB 00:00 (31/52): xz-devel-5.4.4-1.fc39.x86_64.rpm 609 kB/s | 66 kB 00:00 (32/52): zlib-devel-1.2.13-4.fc39.x86_64.rpm 507 kB/s | 45 kB 00:00 (33/52): annobin-docs-12.51-1.fc39.noarch.rpm 249 kB/s | 88 kB 00:00 (34/52): expat-2.6.2-1.fc39.x86_64.rpm 964 kB/s | 114 kB 00:00 (35/52): annobin-plugin-gcc-12.51-1.fc39.x86_64 1.8 MB/s | 959 kB 00:00 (36/52): gcc-plugin-annobin-13.3.1-1.fc39.x86_6 1.2 MB/s | 56 kB 00:00 (37/52): glibc-devel-2.38-18.fc39.x86_64.rpm 1.5 MB/s | 86 kB 00:00 (38/52): glibc-headers-x86-2.38-18.fc39.noarch. 5.9 MB/s | 571 kB 00:00 (39/52): cpp-13.3.1-1.fc39.x86_64.rpm 14 MB/s | 11 MB 00:00 (40/52): pyproject-rpm-macros-1.12.0-1.fc39.noa 706 kB/s | 41 kB 00:00 (41/52): kernel-headers-6.9.4-100.fc39.x86_64.r 7.5 MB/s | 1.6 MB 00:00 (42/52): python-pip-wheel-23.2.1-2.fc39.noarch. 22 MB/s | 1.5 MB 00:00 (43/52): python3-3.12.3-2.fc39.x86_64.rpm 430 kB/s | 27 kB 00:00 (44/52): python3-cython-3.0.6-1.fc39.x86_64.rpm 32 MB/s | 3.8 MB 00:00 (45/52): python3-devel-3.12.3-2.fc39.x86_64.rpm 3.1 MB/s | 313 kB 00:00 (46/52): python3-idna-3.7-1.fc39.noarch.rpm 2.1 MB/s | 116 kB 00:00 (47/52): python3-jinja2-3.1.4-1.fc39.noarch.rpm 7.2 MB/s | 485 kB 00:00 (48/52): python3-urllib3+socks-1.26.18-1.fc39.n 103 kB/s | 10 kB 00:00 (49/52): python3-urllib3-1.26.18-1.fc39.noarch. 3.5 MB/s | 274 kB 00:00 (50/52): python3-libs-3.12.3-2.fc39.x86_64.rpm 34 MB/s | 9.2 MB 00:00 (51/52): tzdata-2024a-2.fc39.noarch.rpm 8.6 MB/s | 715 kB 00:00 (52/52): gcc-13.3.1-1.fc39.x86_64.rpm 31 MB/s | 34 MB 00:01 -------------------------------------------------------------------------------- Total 25 MB/s | 91 MB 00:03 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.12-4.fc39.noarch 1/52 Installing : fonts-filesystem-1:2.0.5-12.fc39.noarch 2/52 Installing : python3-rpm-macros-3.12-4.fc39.noarch 3/52 Installing : libmpc-1.3.1-3.fc39.x86_64 4/52 Installing : cpp-13.3.1-1.fc39.x86_64 5/52 Installing : pyproject-rpm-macros-1.12.0-1.fc39.noarch 6/52 Installing : fontawesome4-fonts-1:4.7.0-19.fc39.noarch 7/52 Installing : google-roboto-slab-fonts-1.100263-0.21.20150923git 8/52 Installing : lato-fonts-2.015-17.fc39.noarch 9/52 Installing : tzdata-2024a-2.fc39.noarch 10/52 Installing : python-pip-wheel-23.2.1-2.fc39.noarch 11/52 Installing : kernel-headers-6.9.4-100.fc39.x86_64 12/52 Installing : glibc-headers-x86-2.38-18.fc39.noarch 13/52 Installing : glibc-devel-2.38-18.fc39.x86_64 14/52 Installing : libxcrypt-devel-4.4.36-2.fc39.x86_64 15/52 Installing : expat-2.6.2-1.fc39.x86_64 16/52 Installing : annobin-docs-12.51-1.fc39.noarch 17/52 Installing : mpdecimal-2.5.1-7.fc39.x86_64 18/52 Installing : libb2-0.98.1-9.fc39.x86_64 19/52 Installing : python3-3.12.3-2.fc39.x86_64 20/52 Installing : python3-libs-3.12.3-2.fc39.x86_64 21/52 Installing : python3-docutils-0.19-5.fc39.noarch 22/52 Installing : python3-packaging-23.1-4.fc39.noarch 23/52 Installing : python3-idna-3.7-1.fc39.noarch 24/52 Installing : python3-rpm-generators-14-7.fc39.noarch 25/52 Installing : python3-babel-2.12.1-6.fc39.noarch 26/52 Installing : python3-charset-normalizer-3.2.0-2.fc39.noarch 27/52 Installing : python3-imagesize-1.4.1-4.fc39.noarch 28/52 Installing : python3-markupsafe-2.1.3-2.fc39.x86_64 29/52 Installing : python3-jinja2-3.1.4-1.fc39.noarch 30/52 Installing : python3-pygments-2.15.1-4.fc39.noarch 31/52 Installing : python3-pysocks-1.7.1-20.fc39.noarch 32/52 Installing : python3-urllib3+socks-1.26.18-1.fc39.noarch 33/52 Installing : python3-urllib3-1.26.18-1.fc39.noarch 34/52 Installing : python3-requests-2.28.2-5.fc39.noarch 35/52 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 36/52 Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 37/52 Installing : python3-sphinx-1:7.2.6-8.fc39.noarch 38/52 Installing : python3-sphinxcontrib-jquery-4.1-3.fc39.noarch 39/52 Installing : gc-8.2.2-4.fc39.x86_64 40/52 Installing : guile22-2.2.7-9.fc39.x86_64 41/52 Installing : make-1:4.4.1-2.fc39.x86_64 42/52 Installing : gcc-13.3.1-1.fc39.x86_64 43/52 Running scriptlet: gcc-13.3.1-1.fc39.x86_64 43/52 Installing : annobin-plugin-gcc-12.51-1.fc39.x86_64 44/52 Running scriptlet: annobin-plugin-gcc-12.51-1.fc39.x86_64 44/52 Installing : gcc-plugin-annobin-13.3.1-1.fc39.x86_64 45/52 Running scriptlet: gcc-plugin-annobin-13.3.1-1.fc39.x86_64 45/52 Installing : python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch 46/52 Installing : python3-devel-3.12.3-2.fc39.x86_64 47/52 Installing : python3-setuptools-67.7.2-7.fc39.noarch 48/52 Installing : python3-cython-3.0.6-1.fc39.x86_64 49/52 Installing : zlib-devel-1.2.13-4.fc39.x86_64 50/52 Installing : xz-devel-5.4.4-1.fc39.x86_64 51/52 Installing : bzip2-devel-1.0.8-16.fc39.x86_64 52/52 Running scriptlet: bzip2-devel-1.0.8-16.fc39.x86_64 52/52 Verifying : python3-sphinx-1:7.2.6-8.fc39.noarch 1/52 Verifying : bzip2-devel-1.0.8-16.fc39.x86_64 2/52 Verifying : fontawesome4-fonts-1:4.7.0-19.fc39.noarch 3/52 Verifying : fonts-filesystem-1:2.0.5-12.fc39.noarch 4/52 Verifying : gc-8.2.2-4.fc39.x86_64 5/52 Verifying : google-roboto-slab-fonts-1.100263-0.21.20150923git 6/52 Verifying : guile22-2.2.7-9.fc39.x86_64 7/52 Verifying : lato-fonts-2.015-17.fc39.noarch 8/52 Verifying : libb2-0.98.1-9.fc39.x86_64 9/52 Verifying : libmpc-1.3.1-3.fc39.x86_64 10/52 Verifying : libxcrypt-devel-4.4.36-2.fc39.x86_64 11/52 Verifying : make-1:4.4.1-2.fc39.x86_64 12/52 Verifying : mpdecimal-2.5.1-7.fc39.x86_64 13/52 Verifying : python-rpm-macros-3.12-4.fc39.noarch 14/52 Verifying : python3-babel-2.12.1-6.fc39.noarch 15/52 Verifying : python3-charset-normalizer-3.2.0-2.fc39.noarch 16/52 Verifying : python3-docutils-0.19-5.fc39.noarch 17/52 Verifying : python3-imagesize-1.4.1-4.fc39.noarch 18/52 Verifying : python3-markupsafe-2.1.3-2.fc39.x86_64 19/52 Verifying : python3-packaging-23.1-4.fc39.noarch 20/52 Verifying : python3-pygments-2.15.1-4.fc39.noarch 21/52 Verifying : python3-pysocks-1.7.1-20.fc39.noarch 22/52 Verifying : python3-requests-2.28.2-5.fc39.noarch 23/52 Verifying : python3-rpm-generators-14-7.fc39.noarch 24/52 Verifying : python3-rpm-macros-3.12-4.fc39.noarch 25/52 Verifying : python3-setuptools-67.7.2-7.fc39.noarch 26/52 Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 27/52 Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 28/52 Verifying : python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch 29/52 Verifying : python3-sphinxcontrib-jquery-4.1-3.fc39.noarch 30/52 Verifying : xz-devel-5.4.4-1.fc39.x86_64 31/52 Verifying : zlib-devel-1.2.13-4.fc39.x86_64 32/52 Verifying : annobin-docs-12.51-1.fc39.noarch 33/52 Verifying : annobin-plugin-gcc-12.51-1.fc39.x86_64 34/52 Verifying : cpp-13.3.1-1.fc39.x86_64 35/52 Verifying : expat-2.6.2-1.fc39.x86_64 36/52 Verifying : gcc-13.3.1-1.fc39.x86_64 37/52 Verifying : gcc-plugin-annobin-13.3.1-1.fc39.x86_64 38/52 Verifying : glibc-devel-2.38-18.fc39.x86_64 39/52 Verifying : glibc-headers-x86-2.38-18.fc39.noarch 40/52 Verifying : kernel-headers-6.9.4-100.fc39.x86_64 41/52 Verifying : pyproject-rpm-macros-1.12.0-1.fc39.noarch 42/52 Verifying : python-pip-wheel-23.2.1-2.fc39.noarch 43/52 Verifying : python3-3.12.3-2.fc39.x86_64 44/52 Verifying : python3-cython-3.0.6-1.fc39.x86_64 45/52 Verifying : python3-devel-3.12.3-2.fc39.x86_64 46/52 Verifying : python3-idna-3.7-1.fc39.noarch 47/52 Verifying : python3-jinja2-3.1.4-1.fc39.noarch 48/52 Verifying : python3-libs-3.12.3-2.fc39.x86_64 49/52 Verifying : python3-urllib3+socks-1.26.18-1.fc39.noarch 50/52 Verifying : python3-urllib3-1.26.18-1.fc39.noarch 51/52 Verifying : tzdata-2024a-2.fc39.noarch 52/52 Installed: annobin-docs-12.51-1.fc39.noarch annobin-plugin-gcc-12.51-1.fc39.x86_64 bzip2-devel-1.0.8-16.fc39.x86_64 cpp-13.3.1-1.fc39.x86_64 expat-2.6.2-1.fc39.x86_64 fontawesome4-fonts-1:4.7.0-19.fc39.noarch fonts-filesystem-1:2.0.5-12.fc39.noarch gc-8.2.2-4.fc39.x86_64 gcc-13.3.1-1.fc39.x86_64 gcc-plugin-annobin-13.3.1-1.fc39.x86_64 glibc-devel-2.38-18.fc39.x86_64 glibc-headers-x86-2.38-18.fc39.noarch google-roboto-slab-fonts-1.100263-0.21.20150923git.fc39.noarch guile22-2.2.7-9.fc39.x86_64 kernel-headers-6.9.4-100.fc39.x86_64 lato-fonts-2.015-17.fc39.noarch libb2-0.98.1-9.fc39.x86_64 libmpc-1.3.1-3.fc39.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-1.12.0-1.fc39.noarch python-pip-wheel-23.2.1-2.fc39.noarch python-rpm-macros-3.12-4.fc39.noarch python3-3.12.3-2.fc39.x86_64 python3-babel-2.12.1-6.fc39.noarch python3-charset-normalizer-3.2.0-2.fc39.noarch python3-cython-3.0.6-1.fc39.x86_64 python3-devel-3.12.3-2.fc39.x86_64 python3-docutils-0.19-5.fc39.noarch python3-idna-3.7-1.fc39.noarch python3-imagesize-1.4.1-4.fc39.noarch python3-jinja2-3.1.4-1.fc39.noarch python3-libs-3.12.3-2.fc39.x86_64 python3-markupsafe-2.1.3-2.fc39.x86_64 python3-packaging-23.1-4.fc39.noarch python3-pygments-2.15.1-4.fc39.noarch python3-pysocks-1.7.1-20.fc39.noarch python3-requests-2.28.2-5.fc39.noarch python3-rpm-generators-14-7.fc39.noarch python3-rpm-macros-3.12-4.fc39.noarch python3-setuptools-67.7.2-7.fc39.noarch python3-snowballstemmer-2.2.0-7.fc39.noarch python3-sphinx-1:7.2.6-8.fc39.noarch python3-sphinx-theme-alabaster-0.7.12-19.fc39.noarch python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch python3-sphinxcontrib-jquery-4.1-3.fc39.noarch python3-urllib3-1.26.18-1.fc39.noarch python3-urllib3+socks-1.26.18-1.fc39.noarch tzdata-2024a-2.fc39.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-0.22.1-1.fc39.src.rpm Start: rpmbuild python-pysam-0.22.1-1.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1718323200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fqqRsY + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.22.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.22.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.22.1 + rm -rf /builddir/build/BUILD/pysam-0.22.1-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/pysam-0.22.1-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-pysam-configure-c99.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcalignedsegment.c pysam/libcalignmentfile.c pysam/libcbcf.c pysam/libcbcftools.c pysam/libcbgzf.c pysam/libcfaidx.c pysam/libchtslib.c pysam/libcsamfile.c pysam/libcsamtools.c pysam/libctabix.c pysam/libctabixproxies.c pysam/libcutils.c pysam/libcvcf.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vxyecZ + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.1 + FORCE_CYTHON=1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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' # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/config.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 top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.cram' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.cram' to be distributed and are already explicitly excluding 'pysam.include.htslib.cram' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.m4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.m4' to be distributed and are already explicitly excluding 'pysam.include.htslib.m4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.os' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.os' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.os' to be distributed and are already explicitly excluding 'pysam.include.htslib.os' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-312/pysam creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.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/sam_mods.c -> 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/hts_check_compile_flags_needed.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -msse4.1 -mpopcnt -mssse3 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o ranlib libhts.a Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.linux-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/sam_mods.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ^ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^ Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.22.1/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.22.1/htslib/htslib/hts.h:37, from /builddir/build/BUILD/pysam-0.22.1/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ 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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gff.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-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ 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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcutils.o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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:2567:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2616:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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:20510:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20510 | (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:37136:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37136 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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 gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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:85892:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85892 | (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:80570:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80570 | (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:44288:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44288 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44314:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44314 | 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:80265:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80265 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/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-0.22.1/pysam -I/builddir/build/BUILD/pysam-0.22.1/htslib -I/builddir/build/BUILD/pysam-0.22.1/samtools -I/builddir/build/BUILD/pysam-0.22.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.1/bcftools -I/builddir/build/BUILD/pysam-0.22.1 -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:30015:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 30015 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24968:10: note: ‘__pyx_v_qual’ was declared here 24968 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.22.1/pysam -L/builddir/build/BUILD/pysam-0.22.1 -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-0.22.1/build/lib.linux-x86_64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.1/build/lib.linux-x86_64-cpython-312 + sphinx-build-3 doc html Running Sphinx v7.2.6 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.Vpd8Ax + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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-0.22.1-1.fc39.x86_64 --prefix /usr # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include copying build/lib.linux-x86_64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.c -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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_check_compile_flags_needed.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc writing byte-compilation script '/tmp/tmpmayqwiwl.py' /usr/bin/python3 /tmp/tmpmayqwiwl.py removing /tmp/tmpmayqwiwl.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam-0.22.1-py3.12.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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 0.22.1-1.fc39 --unique-debug-suffix -0.22.1-1.fc39.x86_64 --unique-debug-src-base python-pysam-0.22.1-1.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.22.1 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-pysam-0.22.1-1.fc39.x86_64 53779 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-0.22.1-1.fc39.x86_64/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.22.1-1.fc39.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.9d35Qt + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.1 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python3-pysam + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.1/README.rst /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.kpRbZd + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.1 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/licenses/python3-pysam + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.1/COPYING /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.1/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.1/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.1/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.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 = 0.22.1-1.fc39 python3-pysam = 0.22.1-1.fc39 python3-pysam(x86-64) = 0.22.1-1.fc39 python3.12-pysam = 0.22.1-1.fc39 python3.12dist(pysam) = 0.22.1 python3dist(pysam) = 0.22.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.1-1.fc39 Processing files: python3-pysam-devel-0.22.1-1.fc39.x86_64 Provides: python-pysam-devel = 0.22.1-1.fc39 python3-pysam-devel = 0.22.1-1.fc39 python3-pysam-devel(x86-64) = 0.22.1-1.fc39 python3.12-pysam-devel = 0.22.1-1.fc39 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-0.22.1-1.fc39.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2GZyiW + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.1 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python-pysam-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/pysam-0.22.1/html /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.1-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.1-1.fc39.x86_64 Provides: python-pysam-debugsource = 0.22.1-1.fc39 python-pysam-debugsource(x86-64) = 0.22.1-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.1-1.fc39.x86_64 Provides: debuginfo(build-id) = 1205cf10e95422b8976692e1433ba72d874aed32 debuginfo(build-id) = 2c64813cccfabb6270751b4b158a4c2b81d9eda7 debuginfo(build-id) = 3597eea335052503b51f06c0e84be764f0106290 debuginfo(build-id) = 7bdc0f78b7a970006ded00df5442f741cfb9f1b7 debuginfo(build-id) = 85d4d124dbb8b28464df858bbb836053b95b9881 debuginfo(build-id) = 8747c3edb5c6af3c2c856f29c5c49d37a8555d59 debuginfo(build-id) = a3588483f29ab7e4588786e1ec90528a23fb554d debuginfo(build-id) = b913107d2b6c48968e74ba813e99d2abfeb425d2 debuginfo(build-id) = b94477ed53248a51b38adf7165cc7c379b521bd9 debuginfo(build-id) = c276b8c51f2f096a1fdb6f7cfbfc1dbcafec77f8 debuginfo(build-id) = e1eb7e5eadd8ca4a8665657d3827090848ec7f77 debuginfo(build-id) = e3df00315805030b0feba4d13b9208fd9d7b05e8 debuginfo(build-id) = feefc4c2f1256428c0e8413630fc9ebff8c2f971 libcalignedsegment.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcalignmentfile.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcbcf.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcbgzf.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcfaidx.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcsamfile.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libctabix.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libctabixproxies.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcutils.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) libcvcf.cpython-312-x86_64-linux-gnu.so-0.22.1-1.fc39.x86_64.debug()(64bit) python-pysam-debuginfo = 0.22.1-1.fc39 python3-pysam-debuginfo = 0.22.1-1.fc39 python3-pysam-debuginfo(x86-64) = 0.22.1-1.fc39 python3.12-pysam-debuginfo = 0.22.1-1.fc39 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) = 0.22.1-1.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.1-1.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.1-1.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.22.1-1.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.1-1.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.1-1.fc39.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.dM5Ne3 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.1-1.fc39.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.l0pZ33 + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/pysam-0.22.1-SPECPARTS + rm -rf pysam-0.22.1 pysam-0.22.1.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-0.22.1-1.fc39.src.rpm Finish: build phase for python-pysam-0.22.1-1.fc39.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.log /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1718739368.112563/root/var/log/dnf.rpm.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.22.1-1.fc39.src.rpm) Config(child) 6 minutes 37 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python-pysam-debugsource", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "x86_64" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "noarch" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "src" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "x86_64" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.22.1", "release": "1.fc39", "arch": "x86_64" } ] } RPMResults finished