Warning: Permanently added '54.145.120.227' (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/6631189-fedora-37-x86_64 --chroot fedora-37-x86_64 Version: 0.69 PID: 6010 Logging PID: 6011 Task: {'appstream': False, 'background': True, 'build_id': 6631189, 'buildroot_pkgs': [], 'chroot': 'fedora-37-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'c2d69f9f16a0540958b35df94f6c14a9f533559c', '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': '0.22.0-1', '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-37-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, 'submitter': 'https://src.fedoraproject.org/user/davidsch', 'tags': [], 'task_id': '6631189-fedora-37-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-3zbq8qlv/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-3zbq8qlv/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam'... Running: git checkout c2d69f9f16a0540958b35df94f6c14a9f533559c -- cmd: ['git', 'checkout', 'c2d69f9f16a0540958b35df94f6c14a9f533559c', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam rc: 0 stdout: stderr: Note: switching to 'c2d69f9f16a0540958b35df94f6c14a9f533559c'. 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 c2d69f9 automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/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-0.22.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o pysam-0.22.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/thrnciar/setuptools-impact-check-control/python-pysam/pysam-0.22.0.tar.gz/md5/f5f8abbff6ba5bfdc15336d89c217f5a/pysam-0.22.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 4522k 100 4522k 0 0 69.1M 0 --:--:-- --:--:-- --:--:-- 70.1M INFO: Reading stdout from command: md5sum pysam-0.22.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1699922217.139082 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1699922217.139082 -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-3zbq8qlv/python-pysam/python-pysam.spec) Config(fedora-37-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.2 INFO: Mock Version: 5.2 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-37-x86_64-bootstrap-1699922217.139082/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:37 INFO: Pulling image: registry.fedoraproject.org/fedora:37 INFO: Copy content of container registry.fedoraproject.org/fedora:37 to /var/lib/mock/fedora-37-x86_64-bootstrap-1699922217.139082/root INFO: Checking that registry.fedoraproject.org/fedora:37 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:37 with podman image mount INFO: image registry.fedoraproject.org/fedora:37 as /var/lib/containers/storage/overlay/8e51bf818a50adbb50d11ee1b0553e87cf49ea7fc0ce771956e23d958a7a1fe8/merged INFO: umounting image registry.fedoraproject.org/fedora:37 (/var/lib/containers/storage/overlay/8e51bf818a50adbb50d11ee1b0553e87cf49ea7fc0ce771956e23d958a7a1fe8/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 5.0 MB/s | 1.2 MB 00:00 fedora 63 MB/s | 82 MB 00:01 updates 54 MB/s | 40 MB 00:00 Package python3-dnf-4.18.0-2.fc37.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.3-1.fc37 updates 322 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc37 updates 156 k python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k python3-dbus x86_64 1.3.2-1.fc37 updates 157 k python3-distro noarch 1.7.0-3.fc37 fedora 48 k python3-six noarch 1.16.0-8.fc37 fedora 42 k python3-systemd x86_64 235-1.fc37 fedora 108 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.2 M Installed size: 3.7 M Downloading Packages: (1/7): python3-distro-1.7.0-3.fc37.noarch.rpm 922 kB/s | 48 kB 00:00 (2/7): python3-six-1.16.0-8.fc37.noarch.rpm 788 kB/s | 42 kB 00:00 (3/7): python3-dateutil-2.8.2-4.fc37.noarch.rpm 4.8 MB/s | 361 kB 00:00 (4/7): dbus-libs-1.14.10-1.fc37.x86_64.rpm 6.7 MB/s | 156 kB 00:00 (5/7): python3-systemd-235-1.fc37.x86_64.rpm 4.3 MB/s | 108 kB 00:00 (6/7): python3-dbus-1.3.2-1.fc37.x86_64.rpm 28 MB/s | 157 kB 00:00 (7/7): python3-dnf-plugins-core-4.4.3-1.fc37.no 30 MB/s | 322 kB 00:00 -------------------------------------------------------------------------------- Total 3.1 MB/s | 1.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : dbus-libs-1:1.14.10-1.fc37.x86_64 1/7 Installing : python3-dbus-1.3.2-1.fc37.x86_64 2/7 Installing : python3-systemd-235-1.fc37.x86_64 3/7 Installing : python3-six-1.16.0-8.fc37.noarch 4/7 Installing : python3-dateutil-1:2.8.2-4.fc37.noarch 5/7 Installing : python3-distro-1.7.0-3.fc37.noarch 6/7 Installing : python3-dnf-plugins-core-4.4.3-1.fc37.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.3-1.fc37.noarch 7/7 Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 1/7 Verifying : python3-distro-1.7.0-3.fc37.noarch 2/7 Verifying : python3-six-1.16.0-8.fc37.noarch 3/7 Verifying : python3-systemd-235-1.fc37.x86_64 4/7 Verifying : dbus-libs-1:1.14.10-1.fc37.x86_64 5/7 Verifying : python3-dbus-1.3.2-1.fc37.x86_64 6/7 Verifying : python3-dnf-plugins-core-4.4.3-1.fc37.noarch 7/7 Installed: dbus-libs-1:1.14.10-1.fc37.x86_64 python3-dateutil-1:2.8.2-4.fc37.noarch python3-dbus-1.3.2-1.fc37.x86_64 python3-distro-1.7.0-3.fc37.noarch python3-dnf-plugins-core-4.4.3-1.fc37.noarch python3-six-1.16.0-8.fc37.noarch python3-systemd-235-1.fc37.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-37-x86_64-1699922217.139082/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 16 MB/s | 1.2 MB 00:00 fedora 63 MB/s | 82 MB 00:01 updates 54 MB/s | 40 MB 00:00 Last metadata expiration check: 0:00:01 ago on Tue Nov 14 00:37:42 2023. Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.15-1.fc37 updates 1.8 M bzip2 x86_64 1.0.8-12.fc37 fedora 52 k coreutils x86_64 9.1-8.fc37 updates 1.1 M cpio x86_64 2.13-13.fc37 fedora 277 k diffutils x86_64 3.8-3.fc37 fedora 378 k fedora-release-common noarch 37-18 updates 19 k findutils x86_64 1:4.9.0-2.fc37 fedora 492 k gawk x86_64 5.1.1-4.fc37 fedora 1.0 M glibc-minimal-langpack x86_64 2.36-14.fc37 updates 79 k grep x86_64 3.7-4.fc37 fedora 273 k gzip x86_64 1.12-2.fc37 fedora 166 k info x86_64 6.8-4.fc37 fedora 225 k patch x86_64 2.7.6-17.fc37 fedora 124 k redhat-rpm-config noarch 229-1.fc37 updates 80 k rpm-build x86_64 4.18.1-2.fc37 updates 75 k sed x86_64 4.8-11.fc37 fedora 306 k shadow-utils x86_64 2:4.12.3-6.fc37 updates 1.3 M tar x86_64 2:1.34-6.fc37 updates 885 k unzip x86_64 6.0-58.fc37 fedora 182 k util-linux x86_64 2.38.1-1.fc37 fedora 2.3 M which x86_64 2.21-39.fc37 updates 42 k xz x86_64 5.4.1-1.fc37 updates 419 k Installing dependencies: alternatives x86_64 1.24-1.fc37 updates 39 k ansible-srpm-macros noarch 1-10.fc37 updates 20 k audit-libs x86_64 3.1.2-1.fc37 updates 117 k authselect x86_64 1.4.2-1.fc37 updates 144 k authselect-libs x86_64 1.4.2-1.fc37 updates 250 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils x86_64 2.38-27.fc37 updates 5.4 M binutils-gold x86_64 2.38-27.fc37 updates 773 k bzip2-libs x86_64 1.0.8-12.fc37 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-1.0.fc37 updates 837 k coreutils-common x86_64 9.1-8.fc37 updates 2.0 M cracklib x86_64 2.9.7-30.fc37 fedora 92 k crypto-policies noarch 20220815-1.gite4ed860.fc37 fedora 86 k curl x86_64 7.85.0-12.fc37 updates 314 k cyrus-sasl-lib x86_64 2.1.28-8.fc37 fedora 792 k debugedit x86_64 5.0-7.fc37 updates 77 k dwz x86_64 0.14-7.fc37 fedora 129 k ed x86_64 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils x86_64 0.189-3.fc37 updates 536 k elfutils-debuginfod-client x86_64 0.189-3.fc37 updates 38 k elfutils-default-yama-scope noarch 0.189-3.fc37 updates 13 k elfutils-libelf x86_64 0.189-3.fc37 updates 194 k elfutils-libs x86_64 0.189-3.fc37 updates 258 k fedora-gpg-keys noarch 37-2 updates 126 k fedora-release noarch 37-18 updates 8.7 k fedora-release-identity-basic noarch 37-18 updates 9.4 k fedora-repos noarch 37-2 updates 9.4 k file x86_64 5.42-4.fc37 fedora 49 k file-libs x86_64 5.42-4.fc37 fedora 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-9.fc37 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 13.2-3.fc37 updates 4.2 M gdbm-libs x86_64 1:1.23-2.fc37 fedora 56 k ghc-srpm-macros noarch 1.6.1-1.fc37 updates 8.0 k glibc x86_64 2.36-14.fc37 updates 2.2 M glibc-common x86_64 2.36-14.fc37 updates 359 k glibc-gconv-extra x86_64 2.36-14.fc37 updates 1.7 M gmp x86_64 1:6.2.1-3.fc37 fedora 315 k gnat-srpm-macros noarch 5-1.fc37 updates 8.3 k go-srpm-macros noarch 3.2.0-1.fc37 fedora 27 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs x86_64 1.6.1-5.fc37 fedora 31 k krb5-libs x86_64 1.19.2-13.fc37 updates 726 k libacl x86_64 2.3.1-4.fc37 fedora 23 k libarchive x86_64 3.6.1-3.fc37 updates 397 k libattr x86_64 2.5.1-5.fc37 fedora 18 k libblkid x86_64 2.38.1-1.fc37 fedora 107 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc37 fedora 67 k libcap-ng x86_64 0.8.3-3.fc37 fedora 33 k libcom_err x86_64 1.46.5-3.fc37 fedora 25 k libcurl x86_64 7.85.0-12.fc37 updates 302 k libdb x86_64 5.3.28-53.fc37 fedora 760 k libeconf x86_64 0.5.2-1.fc37 updates 30 k libevent x86_64 2.1.12-7.fc37 fedora 261 k libfdisk x86_64 2.38.1-1.fc37 fedora 160 k libffi x86_64 3.4.4-1.fc37 updates 37 k libgcc x86_64 12.3.1-1.fc37 updates 113 k libgomp x86_64 12.3.1-1.fc37 updates 301 k libidn2 x86_64 2.3.4-1.fc37 updates 160 k libmount x86_64 2.38.1-1.fc37 fedora 135 k libnghttp2 x86_64 1.51.0-2.fc37 updates 74 k libnsl2 x86_64 2.0.0-4.fc37 fedora 30 k libpkgconf x86_64 1.8.0-3.fc37 fedora 36 k libpsl x86_64 0.21.1-6.fc37 fedora 63 k libpwquality x86_64 1.4.5-3.fc37 updates 119 k libselinux x86_64 3.5-1.fc37 updates 86 k libsemanage x86_64 3.5-2.fc37 updates 120 k libsepol x86_64 3.5-1.fc37 updates 322 k libsigsegv x86_64 2.14-3.fc37 fedora 27 k libsmartcols x86_64 2.38.1-1.fc37 fedora 64 k libssh x86_64 0.10.5-1.fc37 updates 211 k libssh-config noarch 0.10.5-1.fc37 updates 8.6 k libstdc++ x86_64 12.3.1-1.fc37 updates 810 k libtasn1 x86_64 4.19.0-1.fc37 updates 75 k libtirpc x86_64 1.3.3-1.rc1.fc37 updates 93 k libunistring x86_64 1.0-2.fc37 fedora 549 k libutempter x86_64 1.2.1-7.fc37 fedora 26 k libuuid x86_64 2.38.1-1.fc37 fedora 28 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.36-1.fc37 updates 119 k libxml2 x86_64 2.10.4-1.fc37 updates 705 k libzstd x86_64 1.5.5-1.fc37 updates 304 k lua-libs x86_64 5.4.4-9.fc37 updates 132 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs x86_64 1.9.4-1.fc37 updates 67 k mpfr x86_64 4.1.0-10.fc37 fedora 331 k ncurses-base noarch 6.4-3.20230114.fc37 updates 86 k ncurses-libs x86_64 6.4-3.20230114.fc37 updates 329 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap x86_64 2.6.6-1.fc37 updates 253 k openssl-libs x86_64 1:3.0.9-1.fc37 updates 2.1 M p11-kit x86_64 0.25.0-1.fc37 updates 519 k p11-kit-trust x86_64 0.25.0-1.fc37 updates 144 k package-notes-srpm-macros noarch 0.5-7.fc37 updates 11 k pam x86_64 1.5.2-14.fc37 fedora 560 k pam-libs x86_64 1.5.2-14.fc37 fedora 58 k pcre x86_64 8.45-1.fc37.2 fedora 202 k pcre2 x86_64 10.40-1.fc37.1 fedora 236 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-46.fc37 fedora 8.3 k pkgconf x86_64 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config x86_64 1.8.0-3.fc37 fedora 10 k popt x86_64 1.19-1.fc37 fedora 66 k publicsuffix-list-dafsa noarch 20230812-1.fc37 updates 57 k pyproject-srpm-macros noarch 1.10.0-1.fc37 updates 14 k python-srpm-macros noarch 3.11-6.fc37 updates 24 k qt5-srpm-macros noarch 5.15.10-1.fc37 updates 8.2 k readline x86_64 8.2-2.fc37 updates 211 k rpm x86_64 4.18.1-2.fc37 updates 570 k rpm-build-libs x86_64 4.18.1-2.fc37 updates 92 k rpm-libs x86_64 4.18.1-2.fc37 updates 318 k rpmautospec-rpm-macros noarch 0.3.5-1.fc37 updates 9.3 k rust-srpm-macros noarch 25.2-2.fc37 updates 12 k setup noarch 2.14.1-2.fc37 fedora 149 k sqlite-libs x86_64 3.40.0-1.fc37 updates 661 k systemd-libs x86_64 251.14-2.fc37 updates 618 k tzdata noarch 2023c-1.fc37 updates 718 k util-linux-core x86_64 2.38.1-1.fc37 fedora 470 k xxhash-libs x86_64 0.8.2-1.fc37 updates 39 k xz-libs x86_64 5.4.1-1.fc37 updates 109 k zip x86_64 3.0-33.fc37 fedora 259 k zlib x86_64 1.2.12-5.fc37 fedora 94 k zstd x86_64 1.5.5-1.fc37 updates 476 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 151 Packages Total download size: 52 M Installed size: 180 M Downloading Packages: (1/151): basesystem-11-14.fc37.noarch.rpm 136 kB/s | 7.0 kB 00:00 (2/151): bzip2-1.0.8-12.fc37.x86_64.rpm 996 kB/s | 52 kB 00:00 (3/151): bzip2-libs-1.0.8-12.fc37.x86_64.rpm 745 kB/s | 41 kB 00:00 (4/151): cracklib-2.9.7-30.fc37.x86_64.rpm 22 MB/s | 92 kB 00:00 (5/151): cpio-2.13-13.fc37.x86_64.rpm 36 MB/s | 277 kB 00:00 (6/151): crypto-policies-20220815-1.gite4ed860. 16 MB/s | 86 kB 00:00 (7/151): dwz-0.14-7.fc37.x86_64.rpm 30 MB/s | 129 kB 00:00 (8/151): ed-1.18-2.fc37.x86_64.rpm 24 MB/s | 78 kB 00:00 (9/151): efi-srpm-macros-5-6.fc37.noarch.rpm 5.2 MB/s | 22 kB 00:00 (10/151): diffutils-3.8-3.fc37.x86_64.rpm 24 MB/s | 378 kB 00:00 (11/151): file-5.42-4.fc37.x86_64.rpm 15 MB/s | 49 kB 00:00 (12/151): cyrus-sasl-lib-2.1.28-8.fc37.x86_64.r 29 MB/s | 792 kB 00:00 (13/151): findutils-4.9.0-2.fc37.x86_64.rpm 35 MB/s | 492 kB 00:00 (14/151): fonts-srpm-macros-2.0.5-9.fc37.noarch 5.6 MB/s | 26 kB 00:00 (15/151): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 3.3 MB/s | 7.7 kB 00:00 (16/151): file-libs-5.42-4.fc37.x86_64.rpm 21 MB/s | 676 kB 00:00 (17/151): gdbm-libs-1.23-2.fc37.x86_64.rpm 17 MB/s | 56 kB 00:00 (18/151): filesystem-3.18-2.fc37.x86_64.rpm 26 MB/s | 1.1 MB 00:00 (19/151): go-srpm-macros-3.2.0-1.fc37.noarch.rp 7.4 MB/s | 27 kB 00:00 (20/151): gmp-6.2.1-3.fc37.x86_64.rpm 23 MB/s | 315 kB 00:00 (21/151): gzip-1.12-2.fc37.x86_64.rpm 31 MB/s | 166 kB 00:00 (22/151): gawk-5.1.1-4.fc37.x86_64.rpm 38 MB/s | 1.0 MB 00:00 (23/151): kernel-srpm-macros-1.0-15.fc37.noarch 6.1 MB/s | 9.4 kB 00:00 (24/151): grep-3.7-4.fc37.x86_64.rpm 20 MB/s | 273 kB 00:00 (25/151): info-6.8-4.fc37.x86_64.rpm 28 MB/s | 225 kB 00:00 (26/151): keyutils-libs-1.6.1-5.fc37.x86_64.rpm 8.7 MB/s | 31 kB 00:00 (27/151): libacl-2.3.1-4.fc37.x86_64.rpm 8.2 MB/s | 23 kB 00:00 (28/151): libattr-2.5.1-5.fc37.x86_64.rpm 6.9 MB/s | 18 kB 00:00 (29/151): libblkid-2.38.1-1.fc37.x86_64.rpm 25 MB/s | 107 kB 00:00 (30/151): libcap-ng-0.8.3-3.fc37.x86_64.rpm 16 MB/s | 33 kB 00:00 (31/151): libcom_err-1.46.5-3.fc37.x86_64.rpm 11 MB/s | 25 kB 00:00 (32/151): libcap-2.48-5.fc37.x86_64.rpm 9.1 MB/s | 67 kB 00:00 (33/151): libbrotli-1.0.9-9.fc37.x86_64.rpm 33 MB/s | 315 kB 00:00 (34/151): libfdisk-2.38.1-1.fc37.x86_64.rpm 18 MB/s | 160 kB 00:00 (35/151): libevent-2.1.12-7.fc37.x86_64.rpm 18 MB/s | 261 kB 00:00 (36/151): libmount-2.38.1-1.fc37.x86_64.rpm 28 MB/s | 135 kB 00:00 (37/151): libnsl2-2.0.0-4.fc37.x86_64.rpm 11 MB/s | 30 kB 00:00 (38/151): libpkgconf-1.8.0-3.fc37.x86_64.rpm 9.1 MB/s | 36 kB 00:00 (39/151): libpsl-0.21.1-6.fc37.x86_64.rpm 15 MB/s | 63 kB 00:00 (40/151): libsigsegv-2.14-3.fc37.x86_64.rpm 8.9 MB/s | 27 kB 00:00 (41/151): libdb-5.3.28-53.fc37.x86_64.rpm 30 MB/s | 760 kB 00:00 (42/151): libsmartcols-2.38.1-1.fc37.x86_64.rpm 20 MB/s | 64 kB 00:00 (43/151): libutempter-1.2.1-7.fc37.x86_64.rpm 11 MB/s | 26 kB 00:00 (44/151): libuuid-2.38.1-1.fc37.x86_64.rpm 11 MB/s | 28 kB 00:00 (45/151): lua-srpm-macros-1-7.fc37.noarch.rpm 4.8 MB/s | 8.8 kB 00:00 (46/151): libverto-0.3.2-4.fc37.x86_64.rpm 7.9 MB/s | 21 kB 00:00 (47/151): nim-srpm-macros-3-7.fc37.noarch.rpm 5.3 MB/s | 8.4 kB 00:00 (48/151): ocaml-srpm-macros-7-2.fc37.noarch.rpm 6.6 MB/s | 13 kB 00:00 (49/151): openblas-srpm-macros-2-12.fc37.noarch 5.0 MB/s | 7.5 kB 00:00 (50/151): mpfr-4.1.0-10.fc37.x86_64.rpm 37 MB/s | 331 kB 00:00 (51/151): pam-libs-1.5.2-14.fc37.x86_64.rpm 18 MB/s | 58 kB 00:00 (52/151): patch-2.7.6-17.fc37.x86_64.rpm 18 MB/s | 124 kB 00:00 (53/151): libunistring-1.0-2.fc37.x86_64.rpm 21 MB/s | 549 kB 00:00 (54/151): pcre-8.45-1.fc37.2.x86_64.rpm 28 MB/s | 202 kB 00:00 (55/151): pcre2-10.40-1.fc37.1.x86_64.rpm 20 MB/s | 236 kB 00:00 (56/151): pam-1.5.2-14.fc37.x86_64.rpm 21 MB/s | 560 kB 00:00 (57/151): pcre2-syntax-10.40-1.fc37.1.noarch.rp 21 MB/s | 142 kB 00:00 (58/151): perl-srpm-macros-1-46.fc37.noarch.rpm 2.7 MB/s | 8.3 kB 00:00 (59/151): pkgconf-pkg-config-1.8.0-3.fc37.x86_6 5.8 MB/s | 10 kB 00:00 (60/151): pkgconf-1.8.0-3.fc37.x86_64.rpm 8.3 MB/s | 41 kB 00:00 (61/151): popt-1.19-1.fc37.x86_64.rpm 14 MB/s | 66 kB 00:00 (62/151): pkgconf-m4-1.8.0-3.fc37.noarch.rpm 1.6 MB/s | 14 kB 00:00 (63/151): sed-4.8-11.fc37.x86_64.rpm 35 MB/s | 306 kB 00:00 (64/151): setup-2.14.1-2.fc37.noarch.rpm 25 MB/s | 149 kB 00:00 (65/151): unzip-6.0-58.fc37.x86_64.rpm 28 MB/s | 182 kB 00:00 (66/151): util-linux-core-2.38.1-1.fc37.x86_64. 72 MB/s | 470 kB 00:00 (67/151): zip-3.0-33.fc37.x86_64.rpm 39 MB/s | 259 kB 00:00 (68/151): alternatives-1.24-1.fc37.x86_64.rpm 7.6 MB/s | 39 kB 00:00 (69/151): zlib-1.2.12-5.fc37.x86_64.rpm 14 MB/s | 94 kB 00:00 (70/151): ansible-srpm-macros-1-10.fc37.noarch. 6.8 MB/s | 20 kB 00:00 (71/151): audit-libs-3.1.2-1.fc37.x86_64.rpm 28 MB/s | 117 kB 00:00 (72/151): authselect-libs-1.4.2-1.fc37.x86_64.r 24 MB/s | 250 kB 00:00 (73/151): authselect-1.4.2-1.fc37.x86_64.rpm 11 MB/s | 144 kB 00:00 (74/151): util-linux-2.38.1-1.fc37.x86_64.rpm 47 MB/s | 2.3 MB 00:00 (75/151): binutils-gold-2.38-27.fc37.x86_64.rpm 64 MB/s | 773 kB 00:00 (76/151): binutils-2.38-27.fc37.x86_64.rpm 143 MB/s | 5.4 MB 00:00 (77/151): bash-5.2.15-1.fc37.x86_64.rpm 24 MB/s | 1.8 MB 00:00 (78/151): ca-certificates-2023.2.60_v7.0.306-1. 18 MB/s | 837 kB 00:00 (79/151): coreutils-9.1-8.fc37.x86_64.rpm 23 MB/s | 1.1 MB 00:00 (80/151): curl-7.85.0-12.fc37.x86_64.rpm 42 MB/s | 314 kB 00:00 (81/151): debugedit-5.0-7.fc37.x86_64.rpm 21 MB/s | 77 kB 00:00 (82/151): elfutils-debuginfod-client-0.189-3.fc 13 MB/s | 38 kB 00:00 (83/151): elfutils-default-yama-scope-0.189-3.f 5.3 MB/s | 13 kB 00:00 (84/151): elfutils-0.189-3.fc37.x86_64.rpm 42 MB/s | 536 kB 00:00 (85/151): elfutils-libelf-0.189-3.fc37.x86_64.r 32 MB/s | 194 kB 00:00 (86/151): fedora-gpg-keys-37-2.noarch.rpm 16 MB/s | 126 kB 00:00 (87/151): elfutils-libs-0.189-3.fc37.x86_64.rpm 21 MB/s | 258 kB 00:00 (88/151): fedora-release-37-18.noarch.rpm 2.9 MB/s | 8.7 kB 00:00 (89/151): fedora-release-identity-basic-37-18.n 6.2 MB/s | 9.4 kB 00:00 (90/151): fedora-release-common-37-18.noarch.rp 7.2 MB/s | 19 kB 00:00 (91/151): fedora-repos-37-2.noarch.rpm 3.3 MB/s | 9.4 kB 00:00 (92/151): ghc-srpm-macros-1.6.1-1.fc37.noarch.r 4.1 MB/s | 8.0 kB 00:00 (93/151): coreutils-common-9.1-8.fc37.x86_64.rp 34 MB/s | 2.0 MB 00:00 (94/151): glibc-common-2.36-14.fc37.x86_64.rpm 30 MB/s | 359 kB 00:00 (95/151): glibc-2.36-14.fc37.x86_64.rpm 29 MB/s | 2.2 MB 00:00 (96/151): glibc-minimal-langpack-2.36-14.fc37.x 14 MB/s | 79 kB 00:00 (97/151): gnat-srpm-macros-5-1.fc37.noarch.rpm 2.3 MB/s | 8.3 kB 00:00 (98/151): gdb-minimal-13.2-3.fc37.x86_64.rpm 44 MB/s | 4.2 MB 00:00 (99/151): glibc-gconv-extra-2.36-14.fc37.x86_64 26 MB/s | 1.7 MB 00:00 (100/151): libarchive-3.6.1-3.fc37.x86_64.rpm 33 MB/s | 397 kB 00:00 (101/151): libcurl-7.85.0-12.fc37.x86_64.rpm 23 MB/s | 302 kB 00:00 (102/151): libeconf-0.5.2-1.fc37.x86_64.rpm 10 MB/s | 30 kB 00:00 (103/151): krb5-libs-1.19.2-13.fc37.x86_64.rpm 31 MB/s | 726 kB 00:00 (104/151): libffi-3.4.4-1.fc37.x86_64.rpm 13 MB/s | 37 kB 00:00 (105/151): libgcc-12.3.1-1.fc37.x86_64.rpm 28 MB/s | 113 kB 00:00 (106/151): libidn2-2.3.4-1.fc37.x86_64.rpm 37 MB/s | 160 kB 00:00 (107/151): libnghttp2-1.51.0-2.fc37.x86_64.rpm 21 MB/s | 74 kB 00:00 (108/151): libgomp-12.3.1-1.fc37.x86_64.rpm 40 MB/s | 301 kB 00:00 (109/151): libselinux-3.5-1.fc37.x86_64.rpm 23 MB/s | 86 kB 00:00 (110/151): libpwquality-1.4.5-3.fc37.x86_64.rpm 26 MB/s | 119 kB 00:00 (111/151): libsemanage-3.5-2.fc37.x86_64.rpm 13 MB/s | 120 kB 00:00 (112/151): libssh-config-0.10.5-1.fc37.noarch.r 4.1 MB/s | 8.6 kB 00:00 (113/151): libssh-0.10.5-1.fc37.x86_64.rpm 19 MB/s | 211 kB 00:00 (114/151): libsepol-3.5-1.fc37.x86_64.rpm 25 MB/s | 322 kB 00:00 (115/151): libtasn1-4.19.0-1.fc37.x86_64.rpm 14 MB/s | 75 kB 00:00 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python-srpm-macros-3.11-6.fc37.noarc 9.0 MB/s | 24 kB 00:00 (131/151): p11-kit-0.25.0-1.fc37.x86_64.rpm 22 MB/s | 519 kB 00:00 (132/151): qt5-srpm-macros-5.15.10-1.fc37.noarc 4.1 MB/s | 8.2 kB 00:00 (133/151): redhat-rpm-config-229-1.fc37.noarch. 12 MB/s | 80 kB 00:00 (134/151): readline-8.2-2.fc37.x86_64.rpm 27 MB/s | 211 kB 00:00 (135/151): rpm-build-4.18.1-2.fc37.x86_64.rpm 18 MB/s | 75 kB 00:00 (136/151): rpm-build-libs-4.18.1-2.fc37.x86_64. 12 MB/s | 92 kB 00:00 (137/151): rpm-libs-4.18.1-2.fc37.x86_64.rpm 36 MB/s | 318 kB 00:00 (138/151): rpmautospec-rpm-macros-0.3.5-1.fc37. 4.7 MB/s | 9.3 kB 00:00 (139/151): rpm-4.18.1-2.fc37.x86_64.rpm 23 MB/s | 570 kB 00:00 (140/151): rust-srpm-macros-25.2-2.fc37.noarch. 3.3 MB/s | 12 kB 00:00 (141/151): openssl-libs-3.0.9-1.fc37.x86_64.rpm 30 MB/s | 2.1 MB 00:00 (142/151): sqlite-libs-3.40.0-1.fc37.x86_64.rpm 27 MB/s | 661 kB 00:00 (143/151): systemd-libs-251.14-2.fc37.x86_64.rp 37 MB/s | 618 kB 00:00 (144/151): shadow-utils-4.12.3-6.fc37.x86_64.rp 40 MB/s | 1.3 MB 00:00 (145/151): which-2.21-39.fc37.x86_64.rpm 8.9 MB/s | 42 kB 00:00 (146/151): xxhash-libs-0.8.2-1.fc37.x86_64.rpm 9.1 MB/s | 39 kB 00:00 (147/151): tzdata-2023c-1.fc37.noarch.rpm 38 MB/s | 718 kB 00:00 (148/151): tar-1.34-6.fc37.x86_64.rpm 31 MB/s | 885 kB 00:00 (149/151): xz-libs-5.4.1-1.fc37.x86_64.rpm 13 MB/s | 109 kB 00:00 (150/151): xz-5.4.1-1.fc37.x86_64.rpm 23 MB/s | 419 kB 00:00 (151/151): zstd-1.5.5-1.fc37.x86_64.rpm 70 MB/s | 476 kB 00:00 -------------------------------------------------------------------------------- Total 47 MB/s | 52 MB 00:01 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-12.3.1-1.fc37.x86_64 1/151 Running scriptlet: libgcc-12.3.1-1.fc37.x86_64 1/151 Installing : crypto-policies-20220815-1.gite4ed860.fc37.noarc 2/151 Running scriptlet: crypto-policies-20220815-1.gite4ed860.fc37.noarc 2/151 Installing : fedora-release-identity-basic-37-18.noarch 3/151 Installing : tzdata-2023c-1.fc37.noarch 4/151 Installing : rust-srpm-macros-25.2-2.fc37.noarch 5/151 Installing : qt5-srpm-macros-5.15.10-1.fc37.noarch 6/151 Installing : publicsuffix-list-dafsa-20230812-1.fc37.noarch 7/151 Installing : package-notes-srpm-macros-0.5-7.fc37.noarch 8/151 Installing : ncurses-base-6.4-3.20230114.fc37.noarch 9/151 Installing : libssh-config-0.10.5-1.fc37.noarch 10/151 Installing : gnat-srpm-macros-5-1.fc37.noarch 11/151 Installing : ghc-srpm-macros-1.6.1-1.fc37.noarch 12/151 Installing : fedora-gpg-keys-37-2.noarch 13/151 Installing : fedora-release-37-18.noarch 14/151 Installing : fedora-repos-37-2.noarch 15/151 Installing : fedora-release-common-37-18.noarch 16/151 Installing : setup-2.14.1-2.fc37.noarch 17/151 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.1-2.fc37.noarch 17/151 Installing : filesystem-3.18-2.fc37.x86_64 18/151 Installing : basesystem-11-14.fc37.noarch 19/151 Installing : glibc-gconv-extra-2.36-14.fc37.x86_64 20/151 Running scriptlet: glibc-gconv-extra-2.36-14.fc37.x86_64 20/151 Installing : glibc-minimal-langpack-2.36-14.fc37.x86_64 21/151 Installing : glibc-common-2.36-14.fc37.x86_64 22/151 Running scriptlet: glibc-2.36-14.fc37.x86_64 23/151 Installing : glibc-2.36-14.fc37.x86_64 23/151 Running scriptlet: glibc-2.36-14.fc37.x86_64 23/151 Installing : ncurses-libs-6.4-3.20230114.fc37.x86_64 24/151 Installing : bash-5.2.15-1.fc37.x86_64 25/151 Running scriptlet: bash-5.2.15-1.fc37.x86_64 25/151 Installing : zlib-1.2.12-5.fc37.x86_64 26/151 Installing : xz-libs-5.4.1-1.fc37.x86_64 27/151 Installing : bzip2-libs-1.0.8-12.fc37.x86_64 28/151 Installing : libzstd-1.5.5-1.fc37.x86_64 29/151 Installing : elfutils-libelf-0.189-3.fc37.x86_64 30/151 Installing : libuuid-2.38.1-1.fc37.x86_64 31/151 Installing : popt-1.19-1.fc37.x86_64 32/151 Installing : libstdc++-12.3.1-1.fc37.x86_64 33/151 Installing : libblkid-2.38.1-1.fc37.x86_64 34/151 Installing : readline-8.2-2.fc37.x86_64 35/151 Installing : gmp-1:6.2.1-3.fc37.x86_64 36/151 Installing : libattr-2.5.1-5.fc37.x86_64 37/151 Installing : libacl-2.3.1-4.fc37.x86_64 38/151 Installing : libcap-2.48-5.fc37.x86_64 39/151 Installing : libxcrypt-4.4.36-1.fc37.x86_64 40/151 Installing : libeconf-0.5.2-1.fc37.x86_64 41/151 Installing : lz4-libs-1.9.4-1.fc37.x86_64 42/151 Installing : systemd-libs-251.14-2.fc37.x86_64 43/151 Installing : mpfr-4.1.0-10.fc37.x86_64 44/151 Installing : dwz-0.14-7.fc37.x86_64 45/151 Installing : unzip-6.0-58.fc37.x86_64 46/151 Installing : file-libs-5.42-4.fc37.x86_64 47/151 Installing : file-5.42-4.fc37.x86_64 48/151 Installing : sqlite-libs-3.40.0-1.fc37.x86_64 49/151 Installing : libcap-ng-0.8.3-3.fc37.x86_64 50/151 Installing : audit-libs-3.1.2-1.fc37.x86_64 51/151 Installing : pam-libs-1.5.2-14.fc37.x86_64 52/151 Installing : libcom_err-1.46.5-3.fc37.x86_64 53/151 Installing : libsmartcols-2.38.1-1.fc37.x86_64 54/151 Installing : libunistring-1.0-2.fc37.x86_64 55/151 Installing : libidn2-2.3.4-1.fc37.x86_64 56/151 Installing : alternatives-1.24-1.fc37.x86_64 57/151 Installing : libsepol-3.5-1.fc37.x86_64 58/151 Installing : lua-libs-5.4.4-9.fc37.x86_64 59/151 Installing : libpsl-0.21.1-6.fc37.x86_64 60/151 Installing : zip-3.0-33.fc37.x86_64 61/151 Installing : zstd-1.5.5-1.fc37.x86_64 62/151 Installing : libfdisk-2.38.1-1.fc37.x86_64 63/151 Installing : bzip2-1.0.8-12.fc37.x86_64 64/151 Installing : libxml2-2.10.4-1.fc37.x86_64 65/151 Installing : ed-1.18-2.fc37.x86_64 66/151 Installing : elfutils-default-yama-scope-0.189-3.fc37.noarch 67/151 Running scriptlet: elfutils-default-yama-scope-0.189-3.fc37.noarch 67/151 Installing : cpio-2.13-13.fc37.x86_64 68/151 Installing : diffutils-3.8-3.fc37.x86_64 69/151 Installing : gdbm-libs-1:1.23-2.fc37.x86_64 70/151 Installing : cyrus-sasl-lib-2.1.28-8.fc37.x86_64 71/151 Installing : keyutils-libs-1.6.1-5.fc37.x86_64 72/151 Installing : libbrotli-1.0.9-9.fc37.x86_64 73/151 Installing : libdb-5.3.28-53.fc37.x86_64 74/151 Installing : libpkgconf-1.8.0-3.fc37.x86_64 75/151 Installing : pkgconf-1.8.0-3.fc37.x86_64 76/151 Installing : libsigsegv-2.14-3.fc37.x86_64 77/151 Installing : gawk-5.1.1-4.fc37.x86_64 78/151 Installing : libverto-0.3.2-4.fc37.x86_64 79/151 Installing : pcre-8.45-1.fc37.2.x86_64 80/151 Installing : grep-3.7-4.fc37.x86_64 81/151 Installing : xz-5.4.1-1.fc37.x86_64 82/151 Installing : libffi-3.4.4-1.fc37.x86_64 83/151 Installing : p11-kit-0.25.0-1.fc37.x86_64 84/151 Installing : libgomp-12.3.1-1.fc37.x86_64 85/151 Installing : libnghttp2-1.51.0-2.fc37.x86_64 86/151 Installing : libtasn1-4.19.0-1.fc37.x86_64 87/151 Installing : p11-kit-trust-0.25.0-1.fc37.x86_64 88/151 Running scriptlet: p11-kit-trust-0.25.0-1.fc37.x86_64 88/151 Installing : xxhash-libs-0.8.2-1.fc37.x86_64 89/151 Installing : coreutils-common-9.1-8.fc37.x86_64 90/151 Installing : ansible-srpm-macros-1-10.fc37.noarch 91/151 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 92/151 Installing : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 93/151 Installing : perl-srpm-macros-1-46.fc37.noarch 94/151 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 95/151 Installing : pcre2-10.40-1.fc37.1.x86_64 96/151 Installing : libselinux-3.5-1.fc37.x86_64 97/151 Installing : sed-4.8-11.fc37.x86_64 98/151 Installing : findutils-1:4.9.0-2.fc37.x86_64 99/151 Installing : libmount-2.38.1-1.fc37.x86_64 100/151 Installing : util-linux-core-2.38.1-1.fc37.x86_64 101/151 Installing : openssl-libs-1:3.0.9-1.fc37.x86_64 102/151 Installing : coreutils-9.1-8.fc37.x86_64 103/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noar 104/151 Installing : ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noar 104/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noar 104/151 Installing : krb5-libs-1.19.2-13.fc37.x86_64 105/151 Installing : libtirpc-1.3.3-1.rc1.fc37.x86_64 106/151 Installing : gzip-1.12-2.fc37.x86_64 107/151 Running scriptlet: authselect-libs-1.4.2-1.fc37.x86_64 108/151 Installing : authselect-libs-1.4.2-1.fc37.x86_64 108/151 Installing : authselect-1.4.2-1.fc37.x86_64 109/151 Installing : cracklib-2.9.7-30.fc37.x86_64 110/151 Installing : libpwquality-1.4.5-3.fc37.x86_64 111/151 Installing : libnsl2-2.0.0-4.fc37.x86_64 112/151 Installing : pam-1.5.2-14.fc37.x86_64 113/151 Installing : libssh-0.10.5-1.fc37.x86_64 114/151 Installing : libevent-2.1.12-7.fc37.x86_64 115/151 Installing : openldap-2.6.6-1.fc37.x86_64 116/151 Installing : libcurl-7.85.0-12.fc37.x86_64 117/151 Installing : elfutils-debuginfod-client-0.189-3.fc37.x86_64 118/151 Installing : elfutils-libs-0.189-3.fc37.x86_64 119/151 Installing : binutils-gold-2.38-27.fc37.x86_64 120/151 Installing : binutils-2.38-27.fc37.x86_64 121/151 Running scriptlet: binutils-2.38-27.fc37.x86_64 121/151 Installing : elfutils-0.189-3.fc37.x86_64 122/151 Installing : gdb-minimal-13.2-3.fc37.x86_64 123/151 Installing : debugedit-5.0-7.fc37.x86_64 124/151 Installing : curl-7.85.0-12.fc37.x86_64 125/151 Installing : libarchive-3.6.1-3.fc37.x86_64 126/151 Running scriptlet: rpm-4.18.1-2.fc37.x86_64 127/151 Installing : rpm-4.18.1-2.fc37.x86_64 127/151 Installing : rpm-libs-4.18.1-2.fc37.x86_64 128/151 Installing : rpm-build-libs-4.18.1-2.fc37.x86_64 129/151 Installing : efi-srpm-macros-5-6.fc37.noarch 130/151 Installing : lua-srpm-macros-1-7.fc37.noarch 131/151 Installing : rpmautospec-rpm-macros-0.3.5-1.fc37.noarch 132/151 Installing : patch-2.7.6-17.fc37.x86_64 133/151 Installing : libsemanage-3.5-2.fc37.x86_64 134/151 Installing : shadow-utils-2:4.12.3-6.fc37.x86_64 135/151 Running scriptlet: libutempter-1.2.1-7.fc37.x86_64 136/151 Installing : libutempter-1.2.1-7.fc37.x86_64 136/151 Installing : tar-2:1.34-6.fc37.x86_64 137/151 Installing : openblas-srpm-macros-2-12.fc37.noarch 138/151 Installing : ocaml-srpm-macros-7-2.fc37.noarch 139/151 Installing : nim-srpm-macros-3-7.fc37.noarch 140/151 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 141/151 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 142/151 Installing : fonts-srpm-macros-1:2.0.5-9.fc37.noarch 143/151 Installing : go-srpm-macros-3.2.0-1.fc37.noarch 144/151 Installing : python-srpm-macros-3.11-6.fc37.noarch 145/151 Installing : redhat-rpm-config-229-1.fc37.noarch 146/151 Installing : rpm-build-4.18.1-2.fc37.x86_64 147/151 Installing : pyproject-srpm-macros-1.10.0-1.fc37.noarch 148/151 Installing : util-linux-2.38.1-1.fc37.x86_64 149/151 Installing : which-2.21-39.fc37.x86_64 150/151 Installing : info-6.8-4.fc37.x86_64 151/151 Running scriptlet: filesystem-3.18-2.fc37.x86_64 151/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noar 151/151 Running scriptlet: authselect-libs-1.4.2-1.fc37.x86_64 151/151 Running scriptlet: rpm-4.18.1-2.fc37.x86_64 151/151 Running scriptlet: info-6.8-4.fc37.x86_64 151/151 Verifying : basesystem-11-14.fc37.noarch 1/151 Verifying : bzip2-1.0.8-12.fc37.x86_64 2/151 Verifying : bzip2-libs-1.0.8-12.fc37.x86_64 3/151 Verifying : cpio-2.13-13.fc37.x86_64 4/151 Verifying : cracklib-2.9.7-30.fc37.x86_64 5/151 Verifying : crypto-policies-20220815-1.gite4ed860.fc37.noarc 6/151 Verifying : cyrus-sasl-lib-2.1.28-8.fc37.x86_64 7/151 Verifying : diffutils-3.8-3.fc37.x86_64 8/151 Verifying : dwz-0.14-7.fc37.x86_64 9/151 Verifying : ed-1.18-2.fc37.x86_64 10/151 Verifying : efi-srpm-macros-5-6.fc37.noarch 11/151 Verifying : file-5.42-4.fc37.x86_64 12/151 Verifying : file-libs-5.42-4.fc37.x86_64 13/151 Verifying : filesystem-3.18-2.fc37.x86_64 14/151 Verifying : findutils-1:4.9.0-2.fc37.x86_64 15/151 Verifying : fonts-srpm-macros-1:2.0.5-9.fc37.noarch 16/151 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 17/151 Verifying : gawk-5.1.1-4.fc37.x86_64 18/151 Verifying : gdbm-libs-1:1.23-2.fc37.x86_64 19/151 Verifying : gmp-1:6.2.1-3.fc37.x86_64 20/151 Verifying : go-srpm-macros-3.2.0-1.fc37.noarch 21/151 Verifying : grep-3.7-4.fc37.x86_64 22/151 Verifying : gzip-1.12-2.fc37.x86_64 23/151 Verifying : info-6.8-4.fc37.x86_64 24/151 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 25/151 Verifying : keyutils-libs-1.6.1-5.fc37.x86_64 26/151 Verifying : libacl-2.3.1-4.fc37.x86_64 27/151 Verifying : libattr-2.5.1-5.fc37.x86_64 28/151 Verifying : libblkid-2.38.1-1.fc37.x86_64 29/151 Verifying : libbrotli-1.0.9-9.fc37.x86_64 30/151 Verifying : libcap-2.48-5.fc37.x86_64 31/151 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 32/151 Verifying : libcom_err-1.46.5-3.fc37.x86_64 33/151 Verifying : libdb-5.3.28-53.fc37.x86_64 34/151 Verifying : libevent-2.1.12-7.fc37.x86_64 35/151 Verifying : libfdisk-2.38.1-1.fc37.x86_64 36/151 Verifying : libmount-2.38.1-1.fc37.x86_64 37/151 Verifying : libnsl2-2.0.0-4.fc37.x86_64 38/151 Verifying : libpkgconf-1.8.0-3.fc37.x86_64 39/151 Verifying : libpsl-0.21.1-6.fc37.x86_64 40/151 Verifying : libsigsegv-2.14-3.fc37.x86_64 41/151 Verifying : libsmartcols-2.38.1-1.fc37.x86_64 42/151 Verifying : libunistring-1.0-2.fc37.x86_64 43/151 Verifying : libutempter-1.2.1-7.fc37.x86_64 44/151 Verifying : libuuid-2.38.1-1.fc37.x86_64 45/151 Verifying : libverto-0.3.2-4.fc37.x86_64 46/151 Verifying : lua-srpm-macros-1-7.fc37.noarch 47/151 Verifying : mpfr-4.1.0-10.fc37.x86_64 48/151 Verifying : nim-srpm-macros-3-7.fc37.noarch 49/151 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 50/151 Verifying : openblas-srpm-macros-2-12.fc37.noarch 51/151 Verifying : pam-1.5.2-14.fc37.x86_64 52/151 Verifying : pam-libs-1.5.2-14.fc37.x86_64 53/151 Verifying : patch-2.7.6-17.fc37.x86_64 54/151 Verifying : pcre-8.45-1.fc37.2.x86_64 55/151 Verifying : pcre2-10.40-1.fc37.1.x86_64 56/151 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 57/151 Verifying : perl-srpm-macros-1-46.fc37.noarch 58/151 Verifying : pkgconf-1.8.0-3.fc37.x86_64 59/151 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 60/151 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 61/151 Verifying : popt-1.19-1.fc37.x86_64 62/151 Verifying : sed-4.8-11.fc37.x86_64 63/151 Verifying : setup-2.14.1-2.fc37.noarch 64/151 Verifying : unzip-6.0-58.fc37.x86_64 65/151 Verifying : util-linux-2.38.1-1.fc37.x86_64 66/151 Verifying : util-linux-core-2.38.1-1.fc37.x86_64 67/151 Verifying : zip-3.0-33.fc37.x86_64 68/151 Verifying : zlib-1.2.12-5.fc37.x86_64 69/151 Verifying : alternatives-1.24-1.fc37.x86_64 70/151 Verifying : ansible-srpm-macros-1-10.fc37.noarch 71/151 Verifying : audit-libs-3.1.2-1.fc37.x86_64 72/151 Verifying : authselect-1.4.2-1.fc37.x86_64 73/151 Verifying : authselect-libs-1.4.2-1.fc37.x86_64 74/151 Verifying : bash-5.2.15-1.fc37.x86_64 75/151 Verifying : binutils-2.38-27.fc37.x86_64 76/151 Verifying : binutils-gold-2.38-27.fc37.x86_64 77/151 Verifying : ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noar 78/151 Verifying : coreutils-9.1-8.fc37.x86_64 79/151 Verifying : coreutils-common-9.1-8.fc37.x86_64 80/151 Verifying : curl-7.85.0-12.fc37.x86_64 81/151 Verifying : debugedit-5.0-7.fc37.x86_64 82/151 Verifying : elfutils-0.189-3.fc37.x86_64 83/151 Verifying : elfutils-debuginfod-client-0.189-3.fc37.x86_64 84/151 Verifying : elfutils-default-yama-scope-0.189-3.fc37.noarch 85/151 Verifying : elfutils-libelf-0.189-3.fc37.x86_64 86/151 Verifying : elfutils-libs-0.189-3.fc37.x86_64 87/151 Verifying : fedora-gpg-keys-37-2.noarch 88/151 Verifying : fedora-release-37-18.noarch 89/151 Verifying : fedora-release-common-37-18.noarch 90/151 Verifying : fedora-release-identity-basic-37-18.noarch 91/151 Verifying : fedora-repos-37-2.noarch 92/151 Verifying : gdb-minimal-13.2-3.fc37.x86_64 93/151 Verifying : ghc-srpm-macros-1.6.1-1.fc37.noarch 94/151 Verifying : glibc-2.36-14.fc37.x86_64 95/151 Verifying : glibc-common-2.36-14.fc37.x86_64 96/151 Verifying : glibc-gconv-extra-2.36-14.fc37.x86_64 97/151 Verifying : glibc-minimal-langpack-2.36-14.fc37.x86_64 98/151 Verifying : gnat-srpm-macros-5-1.fc37.noarch 99/151 Verifying : krb5-libs-1.19.2-13.fc37.x86_64 100/151 Verifying : libarchive-3.6.1-3.fc37.x86_64 101/151 Verifying : libcurl-7.85.0-12.fc37.x86_64 102/151 Verifying : libeconf-0.5.2-1.fc37.x86_64 103/151 Verifying : libffi-3.4.4-1.fc37.x86_64 104/151 Verifying : libgcc-12.3.1-1.fc37.x86_64 105/151 Verifying : libgomp-12.3.1-1.fc37.x86_64 106/151 Verifying : libidn2-2.3.4-1.fc37.x86_64 107/151 Verifying : libnghttp2-1.51.0-2.fc37.x86_64 108/151 Verifying : libpwquality-1.4.5-3.fc37.x86_64 109/151 Verifying : libselinux-3.5-1.fc37.x86_64 110/151 Verifying : libsemanage-3.5-2.fc37.x86_64 111/151 Verifying : libsepol-3.5-1.fc37.x86_64 112/151 Verifying : libssh-0.10.5-1.fc37.x86_64 113/151 Verifying : libssh-config-0.10.5-1.fc37.noarch 114/151 Verifying : libstdc++-12.3.1-1.fc37.x86_64 115/151 Verifying : libtasn1-4.19.0-1.fc37.x86_64 116/151 Verifying : libtirpc-1.3.3-1.rc1.fc37.x86_64 117/151 Verifying : libxcrypt-4.4.36-1.fc37.x86_64 118/151 Verifying : libxml2-2.10.4-1.fc37.x86_64 119/151 Verifying : libzstd-1.5.5-1.fc37.x86_64 120/151 Verifying : lua-libs-5.4.4-9.fc37.x86_64 121/151 Verifying : lz4-libs-1.9.4-1.fc37.x86_64 122/151 Verifying : ncurses-base-6.4-3.20230114.fc37.noarch 123/151 Verifying : ncurses-libs-6.4-3.20230114.fc37.x86_64 124/151 Verifying : openldap-2.6.6-1.fc37.x86_64 125/151 Verifying : openssl-libs-1:3.0.9-1.fc37.x86_64 126/151 Verifying : p11-kit-0.25.0-1.fc37.x86_64 127/151 Verifying : p11-kit-trust-0.25.0-1.fc37.x86_64 128/151 Verifying : package-notes-srpm-macros-0.5-7.fc37.noarch 129/151 Verifying : publicsuffix-list-dafsa-20230812-1.fc37.noarch 130/151 Verifying : pyproject-srpm-macros-1.10.0-1.fc37.noarch 131/151 Verifying : python-srpm-macros-3.11-6.fc37.noarch 132/151 Verifying : qt5-srpm-macros-5.15.10-1.fc37.noarch 133/151 Verifying : readline-8.2-2.fc37.x86_64 134/151 Verifying : redhat-rpm-config-229-1.fc37.noarch 135/151 Verifying : rpm-4.18.1-2.fc37.x86_64 136/151 Verifying : rpm-build-4.18.1-2.fc37.x86_64 137/151 Verifying : rpm-build-libs-4.18.1-2.fc37.x86_64 138/151 Verifying : rpm-libs-4.18.1-2.fc37.x86_64 139/151 Verifying : rpmautospec-rpm-macros-0.3.5-1.fc37.noarch 140/151 Verifying : rust-srpm-macros-25.2-2.fc37.noarch 141/151 Verifying : shadow-utils-2:4.12.3-6.fc37.x86_64 142/151 Verifying : sqlite-libs-3.40.0-1.fc37.x86_64 143/151 Verifying : systemd-libs-251.14-2.fc37.x86_64 144/151 Verifying : tar-2:1.34-6.fc37.x86_64 145/151 Verifying : tzdata-2023c-1.fc37.noarch 146/151 Verifying : which-2.21-39.fc37.x86_64 147/151 Verifying : xxhash-libs-0.8.2-1.fc37.x86_64 148/151 Verifying : xz-5.4.1-1.fc37.x86_64 149/151 Verifying : xz-libs-5.4.1-1.fc37.x86_64 150/151 Verifying : zstd-1.5.5-1.fc37.x86_64 151/151 Installed: alternatives-1.24-1.fc37.x86_64 ansible-srpm-macros-1-10.fc37.noarch audit-libs-3.1.2-1.fc37.x86_64 authselect-1.4.2-1.fc37.x86_64 authselect-libs-1.4.2-1.fc37.x86_64 basesystem-11-14.fc37.noarch bash-5.2.15-1.fc37.x86_64 binutils-2.38-27.fc37.x86_64 binutils-gold-2.38-27.fc37.x86_64 bzip2-1.0.8-12.fc37.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noarch coreutils-9.1-8.fc37.x86_64 coreutils-common-9.1-8.fc37.x86_64 cpio-2.13-13.fc37.x86_64 cracklib-2.9.7-30.fc37.x86_64 crypto-policies-20220815-1.gite4ed860.fc37.noarch curl-7.85.0-12.fc37.x86_64 cyrus-sasl-lib-2.1.28-8.fc37.x86_64 debugedit-5.0-7.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.14-7.fc37.x86_64 ed-1.18-2.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.189-3.fc37.x86_64 elfutils-debuginfod-client-0.189-3.fc37.x86_64 elfutils-default-yama-scope-0.189-3.fc37.noarch elfutils-libelf-0.189-3.fc37.x86_64 elfutils-libs-0.189-3.fc37.x86_64 fedora-gpg-keys-37-2.noarch fedora-release-37-18.noarch fedora-release-common-37-18.noarch fedora-release-identity-basic-37-18.noarch fedora-repos-37-2.noarch file-5.42-4.fc37.x86_64 file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc37.x86_64 fonts-srpm-macros-1:2.0.5-9.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.x86_64 gdb-minimal-13.2-3.fc37.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 ghc-srpm-macros-1.6.1-1.fc37.noarch glibc-2.36-14.fc37.x86_64 glibc-common-2.36-14.fc37.x86_64 glibc-gconv-extra-2.36-14.fc37.x86_64 glibc-minimal-langpack-2.36-14.fc37.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnat-srpm-macros-5-1.fc37.noarch go-srpm-macros-3.2.0-1.fc37.noarch grep-3.7-4.fc37.x86_64 gzip-1.12-2.fc37.x86_64 info-6.8-4.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.19.2-13.fc37.x86_64 libacl-2.3.1-4.fc37.x86_64 libarchive-3.6.1-3.fc37.x86_64 libattr-2.5.1-5.fc37.x86_64 libblkid-2.38.1-1.fc37.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcurl-7.85.0-12.fc37.x86_64 libdb-5.3.28-53.fc37.x86_64 libeconf-0.5.2-1.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 libfdisk-2.38.1-1.fc37.x86_64 libffi-3.4.4-1.fc37.x86_64 libgcc-12.3.1-1.fc37.x86_64 libgomp-12.3.1-1.fc37.x86_64 libidn2-2.3.4-1.fc37.x86_64 libmount-2.38.1-1.fc37.x86_64 libnghttp2-1.51.0-2.fc37.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 libpwquality-1.4.5-3.fc37.x86_64 libselinux-3.5-1.fc37.x86_64 libsemanage-3.5-2.fc37.x86_64 libsepol-3.5-1.fc37.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-1.fc37.x86_64 libssh-0.10.5-1.fc37.x86_64 libssh-config-0.10.5-1.fc37.noarch libstdc++-12.3.1-1.fc37.x86_64 libtasn1-4.19.0-1.fc37.x86_64 libtirpc-1.3.3-1.rc1.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 libuuid-2.38.1-1.fc37.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.36-1.fc37.x86_64 libxml2-2.10.4-1.fc37.x86_64 libzstd-1.5.5-1.fc37.x86_64 lua-libs-5.4.4-9.fc37.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.4-1.fc37.x86_64 mpfr-4.1.0-10.fc37.x86_64 ncurses-base-6.4-3.20230114.fc37.noarch ncurses-libs-6.4-3.20230114.fc37.x86_64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.6-1.fc37.x86_64 openssl-libs-1:3.0.9-1.fc37.x86_64 p11-kit-0.25.0-1.fc37.x86_64 p11-kit-trust-0.25.0-1.fc37.x86_64 package-notes-srpm-macros-0.5-7.fc37.noarch pam-1.5.2-14.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 patch-2.7.6-17.fc37.x86_64 pcre-8.45-1.fc37.2.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc37.x86_64 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.x86_64 popt-1.19-1.fc37.x86_64 publicsuffix-list-dafsa-20230812-1.fc37.noarch pyproject-srpm-macros-1.10.0-1.fc37.noarch python-srpm-macros-3.11-6.fc37.noarch qt5-srpm-macros-5.15.10-1.fc37.noarch readline-8.2-2.fc37.x86_64 redhat-rpm-config-229-1.fc37.noarch rpm-4.18.1-2.fc37.x86_64 rpm-build-4.18.1-2.fc37.x86_64 rpm-build-libs-4.18.1-2.fc37.x86_64 rpm-libs-4.18.1-2.fc37.x86_64 rpmautospec-rpm-macros-0.3.5-1.fc37.noarch rust-srpm-macros-25.2-2.fc37.noarch sed-4.8-11.fc37.x86_64 setup-2.14.1-2.fc37.noarch shadow-utils-2:4.12.3-6.fc37.x86_64 sqlite-libs-3.40.0-1.fc37.x86_64 systemd-libs-251.14-2.fc37.x86_64 tar-2:1.34-6.fc37.x86_64 tzdata-2023c-1.fc37.noarch unzip-6.0-58.fc37.x86_64 util-linux-2.38.1-1.fc37.x86_64 util-linux-core-2.38.1-1.fc37.x86_64 which-2.21-39.fc37.x86_64 xxhash-libs-0.8.2-1.fc37.x86_64 xz-5.4.1-1.fc37.x86_64 xz-libs-5.4.1-1.fc37.x86_64 zip-3.0-33.fc37.x86_64 zlib-1.2.12-5.fc37.x86_64 zstd-1.5.5-1.fc37.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-1.24-1.fc37.x86_64 ansible-srpm-macros-1-10.fc37.noarch audit-libs-3.1.2-1.fc37.x86_64 authselect-1.4.2-1.fc37.x86_64 authselect-libs-1.4.2-1.fc37.x86_64 basesystem-11-14.fc37.noarch bash-5.2.15-1.fc37.x86_64 binutils-2.38-27.fc37.x86_64 binutils-gold-2.38-27.fc37.x86_64 bzip2-1.0.8-12.fc37.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 ca-certificates-2023.2.60_v7.0.306-1.0.fc37.noarch coreutils-9.1-8.fc37.x86_64 coreutils-common-9.1-8.fc37.x86_64 cpio-2.13-13.fc37.x86_64 cracklib-2.9.7-30.fc37.x86_64 crypto-policies-20220815-1.gite4ed860.fc37.noarch curl-7.85.0-12.fc37.x86_64 cyrus-sasl-lib-2.1.28-8.fc37.x86_64 debugedit-5.0-7.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.14-7.fc37.x86_64 ed-1.18-2.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.189-3.fc37.x86_64 elfutils-debuginfod-client-0.189-3.fc37.x86_64 elfutils-default-yama-scope-0.189-3.fc37.noarch elfutils-libelf-0.189-3.fc37.x86_64 elfutils-libs-0.189-3.fc37.x86_64 fedora-gpg-keys-37-2.noarch fedora-release-37-18.noarch fedora-release-common-37-18.noarch fedora-release-identity-basic-37-18.noarch fedora-repos-37-2.noarch file-5.42-4.fc37.x86_64 file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-4.9.0-2.fc37.x86_64 fonts-srpm-macros-2.0.5-9.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.x86_64 gdb-minimal-13.2-3.fc37.x86_64 gdbm-libs-1.23-2.fc37.x86_64 ghc-srpm-macros-1.6.1-1.fc37.noarch glibc-2.36-14.fc37.x86_64 glibc-common-2.36-14.fc37.x86_64 glibc-gconv-extra-2.36-14.fc37.x86_64 glibc-minimal-langpack-2.36-14.fc37.x86_64 gmp-6.2.1-3.fc37.x86_64 gnat-srpm-macros-5-1.fc37.noarch go-srpm-macros-3.2.0-1.fc37.noarch gpg-pubkey-5323552a-6112bcdc grep-3.7-4.fc37.x86_64 gzip-1.12-2.fc37.x86_64 info-6.8-4.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.19.2-13.fc37.x86_64 libacl-2.3.1-4.fc37.x86_64 libarchive-3.6.1-3.fc37.x86_64 libattr-2.5.1-5.fc37.x86_64 libblkid-2.38.1-1.fc37.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcurl-7.85.0-12.fc37.x86_64 libdb-5.3.28-53.fc37.x86_64 libeconf-0.5.2-1.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 libfdisk-2.38.1-1.fc37.x86_64 libffi-3.4.4-1.fc37.x86_64 libgcc-12.3.1-1.fc37.x86_64 libgomp-12.3.1-1.fc37.x86_64 libidn2-2.3.4-1.fc37.x86_64 libmount-2.38.1-1.fc37.x86_64 libnghttp2-1.51.0-2.fc37.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 libpwquality-1.4.5-3.fc37.x86_64 libselinux-3.5-1.fc37.x86_64 libsemanage-3.5-2.fc37.x86_64 libsepol-3.5-1.fc37.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-1.fc37.x86_64 libssh-0.10.5-1.fc37.x86_64 libssh-config-0.10.5-1.fc37.noarch libstdc++-12.3.1-1.fc37.x86_64 libtasn1-4.19.0-1.fc37.x86_64 libtirpc-1.3.3-1.rc1.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 libuuid-2.38.1-1.fc37.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.36-1.fc37.x86_64 libxml2-2.10.4-1.fc37.x86_64 libzstd-1.5.5-1.fc37.x86_64 lua-libs-5.4.4-9.fc37.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.4-1.fc37.x86_64 mpfr-4.1.0-10.fc37.x86_64 ncurses-base-6.4-3.20230114.fc37.noarch ncurses-libs-6.4-3.20230114.fc37.x86_64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.6-1.fc37.x86_64 openssl-libs-3.0.9-1.fc37.x86_64 p11-kit-0.25.0-1.fc37.x86_64 p11-kit-trust-0.25.0-1.fc37.x86_64 package-notes-srpm-macros-0.5-7.fc37.noarch pam-1.5.2-14.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 patch-2.7.6-17.fc37.x86_64 pcre-8.45-1.fc37.2.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc37.x86_64 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.x86_64 popt-1.19-1.fc37.x86_64 publicsuffix-list-dafsa-20230812-1.fc37.noarch pyproject-srpm-macros-1.10.0-1.fc37.noarch python-srpm-macros-3.11-6.fc37.noarch qt5-srpm-macros-5.15.10-1.fc37.noarch readline-8.2-2.fc37.x86_64 redhat-rpm-config-229-1.fc37.noarch rpm-4.18.1-2.fc37.x86_64 rpm-build-4.18.1-2.fc37.x86_64 rpm-build-libs-4.18.1-2.fc37.x86_64 rpm-libs-4.18.1-2.fc37.x86_64 rpmautospec-rpm-macros-0.3.5-1.fc37.noarch rust-srpm-macros-25.2-2.fc37.noarch sed-4.8-11.fc37.x86_64 setup-2.14.1-2.fc37.noarch shadow-utils-4.12.3-6.fc37.x86_64 sqlite-libs-3.40.0-1.fc37.x86_64 systemd-libs-251.14-2.fc37.x86_64 tar-1.34-6.fc37.x86_64 tzdata-2023c-1.fc37.noarch unzip-6.0-58.fc37.x86_64 util-linux-2.38.1-1.fc37.x86_64 util-linux-core-2.38.1-1.fc37.x86_64 which-2.21-39.fc37.x86_64 xxhash-libs-0.8.2-1.fc37.x86_64 xz-5.4.1-1.fc37.x86_64 xz-libs-5.4.1-1.fc37.x86_64 zip-3.0-33.fc37.x86_64 zlib-1.2.12-5.fc37.x86_64 zstd-1.5.5-1.fc37.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1699920000 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-1.fc37.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.rpm.log /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.librepo.log /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-3zbq8qlv/python-pysam/python-pysam.spec) Config(child) 1 minutes 1 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-0.22.0-1.fc37.src.rpm) Config(fedora-37-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-37-x86_64-bootstrap-1699922217.139082/root. INFO: reusing tmpfs at /var/lib/mock/fedora-37-x86_64-bootstrap-1699922217.139082/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-37-x86_64-1699922217.139082/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.18.1-2.fc37.x86_64 python3-dnf-4.18.0-2.fc37.noarch python3-dnf-plugins-core-4.4.3-1.fc37.noarch yum-4.18.0-2.fc37.noarch Start: build phase for python-pysam-0.22.0-1.fc37.src.rpm Start: build setup for python-pysam-0.22.0-1.fc37.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1699920000 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-1.fc37.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 88 kB/s | 2.2 kB 00:00 fedora 174 kB/s | 27 kB 00:00 updates 173 kB/s | 25 kB 00:00 Dependencies resolved. ================================================================================================ Package Arch Version Repo Size ================================================================================================ Installing: bzip2-devel x86_64 1.0.8-12.fc37 fedora 214 k gcc x86_64 12.3.1-1.fc37 updates 33 M python3-Cython x86_64 0.29.32-2.fc37 updates 2.6 M python3-devel x86_64 3.11.6-1.fc37 updates 270 k python3-setuptools noarch 62.6.0-3.fc37 updates 1.6 M python3-sphinx noarch 1:5.1.1-1.fc37 copr_base 2.6 M python3-sphinx_rtd_theme noarch 1.0.0-8.fc37 fedora 79 k xz-devel x86_64 5.4.1-1.fc37 updates 65 k zlib-devel x86_64 1.2.12-5.fc37 fedora 44 k Installing dependencies: annobin-docs noarch 12.28-1.fc37 updates 91 k annobin-plugin-gcc x86_64 12.28-1.fc37 updates 957 k cpp x86_64 12.3.1-1.fc37 updates 11 M expat x86_64 2.5.0-1.fc37 updates 110 k fontawesome-fonts noarch 1:4.7.0-14.fc37 fedora 204 k fonts-filesystem noarch 1:2.0.5-9.fc37 fedora 7.9 k gc x86_64 8.0.6-4.fc37 fedora 103 k gcc-plugin-annobin x86_64 12.3.1-1.fc37 updates 59 k glibc-devel x86_64 2.36-14.fc37 updates 92 k glibc-headers-x86 noarch 2.36-14.fc37 updates 573 k google-roboto-slab-fonts noarch 1.100263-0.18.20150923git.fc37 fedora 239 k guile22 x86_64 2.2.7-6.fc37 fedora 6.5 M kernel-headers x86_64 6.5.4-100.fc37 updates 1.5 M lato-fonts noarch 2.015-14.fc37 fedora 3.1 M libb2 x86_64 0.98.1-7.fc37 fedora 25 k libmpc x86_64 1.2.1-5.fc37 fedora 61 k libtool-ltdl x86_64 2.4.7-2.fc37 fedora 37 k libxcrypt-devel x86_64 4.4.36-1.fc37 updates 29 k make x86_64 1:4.3-11.fc37 fedora 542 k mpdecimal x86_64 2.5.1-4.fc37 fedora 102 k pyproject-rpm-macros noarch 1.10.0-1.fc37 updates 41 k python-pip-wheel noarch 22.2.2-3.fc37 updates 1.4 M python-rpm-macros noarch 3.11-6.fc37 updates 19 k python-setuptools-wheel noarch 62.6.0-3.fc37 updates 711 k python3 x86_64 3.11.6-1.fc37 updates 28 k python3-babel noarch 2.10.3-3.fc37 fedora 6.5 M python3-charset-normalizer noarch 2.1.0-2.fc37 fedora 102 k python3-docutils noarch 0.18.1-2.fc37 fedora 1.1 M python3-idna noarch 3.3-4.fc37 fedora 110 k python3-imagesize noarch 1.2.0-9.fc37 fedora 20 k python3-jinja2 noarch 3.0.3-5.fc37 fedora 630 k python3-libs x86_64 3.11.6-1.fc37 updates 9.6 M python3-markupsafe x86_64 2.1.1-3.fc37 fedora 30 k python3-packaging noarch 21.3-6.fc37 fedora 98 k python3-pygments noarch 2.12.0-4.fc37 fedora 2.4 M python3-pyparsing noarch 3.0.9-2.fc37 fedora 262 k python3-pysocks noarch 1.7.1-15.fc37 fedora 40 k python3-pytz noarch 2023.3.post1-1.fc37 updates 65 k python3-requests noarch 2.28.1-3.fc37 updates 155 k python3-rpm-generators noarch 13-3.fc37 updates 29 k python3-rpm-macros noarch 3.11-6.fc37 updates 14 k python3-six noarch 1.16.0-8.fc37 fedora 42 k python3-snowballstemmer noarch 2.2.0-2.fc37 fedora 256 k python3-sphinx-theme-alabaster noarch 0.7.12-16.fc37 fedora 29 k python3-sphinxcontrib-applehelp noarch 1.0.2-10.fc37 fedora 48 k python3-sphinxcontrib-devhelp noarch 1.0.2-10.fc37 fedora 42 k python3-sphinxcontrib-htmlhelp noarch 2.0.0-7.fc37 fedora 55 k python3-sphinxcontrib-jsmath noarch 1.0.1-18.fc37 fedora 17 k python3-sphinxcontrib-qthelp noarch 1.0.3-11.fc37 fedora 48 k python3-sphinxcontrib-serializinghtml noarch 1.1.5-6.fc37 fedora 48 k python3-urllib3 noarch 1.26.18-1.fc37 updates 258 k python3-urllib3+socks noarch 1.26.18-1.fc37 updates 9.6 k Transaction Summary ================================================================================================ Install 61 Packages Total download size: 90 M Installed size: 326 M Downloading Packages: (1/61): bzip2-devel-1.0.8-12.fc37.x86_64.rpm 3.8 MB/s | 214 kB 00:00 (2/61): fontawesome-fonts-4.7.0-14.fc37.noarch. 3.4 MB/s | 204 kB 00:00 (3/61): fonts-filesystem-2.0.5-9.fc37.noarch.rp 872 kB/s | 7.9 kB 00:00 (4/61): gc-8.0.6-4.fc37.x86_64.rpm 11 MB/s | 103 kB 00:00 (5/61): google-roboto-slab-fonts-1.100263-0.18. 22 MB/s | 239 kB 00:00 (6/61): guile22-2.2.7-6.fc37.x86_64.rpm 64 MB/s | 6.5 MB 00:00 (7/61): libb2-0.98.1-7.fc37.x86_64.rpm 4.3 MB/s | 25 kB 00:00 (8/61): libmpc-1.2.1-5.fc37.x86_64.rpm 23 MB/s | 61 kB 00:00 (9/61): libtool-ltdl-2.4.7-2.fc37.x86_64.rpm 16 MB/s | 37 kB 00:00 (10/61): make-4.3-11.fc37.x86_64.rpm 64 MB/s | 542 kB 00:00 (11/61): mpdecimal-2.5.1-4.fc37.x86_64.rpm 12 MB/s | 102 kB 00:00 (12/61): python3-sphinx-5.1.1-1.fc37.noarch.rpm 11 MB/s | 2.6 MB 00:00 (13/61): python3-charset-normalizer-2.1.0-2.fc3 26 MB/s | 102 kB 00:00 (14/61): python3-docutils-0.18.1-2.fc37.noarch. 39 MB/s | 1.1 MB 00:00 (15/61): lato-fonts-2.015-14.fc37.noarch.rpm 16 MB/s | 3.1 MB 00:00 (16/61): python3-idna-3.3-4.fc37.noarch.rpm 15 MB/s | 110 kB 00:00 (17/61): python3-imagesize-1.2.0-9.fc37.noarch. 5.1 MB/s | 20 kB 00:00 (18/61): python3-markupsafe-2.1.1-3.fc37.x86_64 6.4 MB/s | 30 kB 00:00 (19/61): python3-jinja2-3.0.3-5.fc37.noarch.rpm 49 MB/s | 630 kB 00:00 (20/61): python3-packaging-21.3-6.fc37.noarch.r 20 MB/s | 98 kB 00:00 (21/61): python3-pyparsing-3.0.9-2.fc37.noarch. 20 MB/s | 262 kB 00:00 (22/61): python3-pysocks-1.7.1-15.fc37.noarch.r 6.2 MB/s | 40 kB 00:00 (23/61): python3-six-1.16.0-8.fc37.noarch.rpm 6.6 MB/s | 42 kB 00:00 (24/61): python3-snowballstemmer-2.2.0-2.fc37.n 22 MB/s | 256 kB 00:00 (25/61): python3-sphinx-theme-alabaster-0.7.12- 8.8 MB/s | 29 kB 00:00 (26/61): python3-sphinx_rtd_theme-1.0.0-8.fc37. 7.7 MB/s | 79 kB 00:00 (27/61): python3-sphinxcontrib-applehelp-1.0.2- 13 MB/s | 48 kB 00:00 (28/61): python3-pygments-2.12.0-4.fc37.noarch. 40 MB/s | 2.4 MB 00:00 (29/61): python3-sphinxcontrib-devhelp-1.0.2-10 9.1 MB/s | 42 kB 00:00 (30/61): python3-sphinxcontrib-htmlhelp-2.0.0-7 14 MB/s | 55 kB 00:00 (31/61): python3-sphinxcontrib-jsmath-1.0.1-18. 4.3 MB/s | 17 kB 00:00 (32/61): python3-sphinxcontrib-qthelp-1.0.3-11. 9.8 MB/s | 48 kB 00:00 (33/61): python3-sphinxcontrib-serializinghtml- 9.2 MB/s | 48 kB 00:00 (34/61): annobin-docs-12.28-1.fc37.noarch.rpm 18 MB/s | 91 kB 00:00 (35/61): zlib-devel-1.2.12-5.fc37.x86_64.rpm 7.1 MB/s | 44 kB 00:00 (36/61): annobin-plugin-gcc-12.28-1.fc37.x86_64 49 MB/s | 957 kB 00:00 (37/61): expat-2.5.0-1.fc37.x86_64.rpm 16 MB/s | 110 kB 00:00 (38/61): python3-babel-2.10.3-3.fc37.noarch.rpm 30 MB/s | 6.5 MB 00:00 (39/61): gcc-plugin-annobin-12.3.1-1.fc37.x86_6 20 MB/s | 59 kB 00:00 (40/61): glibc-devel-2.36-14.fc37.x86_64.rpm 23 MB/s | 92 kB 00:00 (41/61): glibc-headers-x86-2.36-14.fc37.noarch. 34 MB/s | 573 kB 00:00 (42/61): kernel-headers-6.5.4-100.fc37.x86_64.r 117 MB/s | 1.5 MB 00:00 (43/61): libxcrypt-devel-4.4.36-1.fc37.x86_64.r 6.2 MB/s | 29 kB 00:00 (44/61): pyproject-rpm-macros-1.10.0-1.fc37.noa 11 MB/s | 41 kB 00:00 (45/61): python-pip-wheel-22.2.2-3.fc37.noarch. 101 MB/s | 1.4 MB 00:00 (46/61): python-rpm-macros-3.11-6.fc37.noarch.r 5.7 MB/s | 19 kB 00:00 (47/61): python-setuptools-wheel-62.6.0-3.fc37. 92 MB/s | 711 kB 00:00 (48/61): python3-3.11.6-1.fc37.x86_64.rpm 5.7 MB/s | 28 kB 00:00 (49/61): python3-Cython-0.29.32-2.fc37.x86_64.r 38 MB/s | 2.6 MB 00:00 (50/61): cpp-12.3.1-1.fc37.x86_64.rpm 50 MB/s | 11 MB 00:00 (51/61): python3-devel-3.11.6-1.fc37.x86_64.rpm 22 MB/s | 270 kB 00:00 (52/61): python3-pytz-2023.3.post1-1.fc37.noarc 7.2 MB/s | 65 kB 00:00 (53/61): python3-requests-2.28.1-3.fc37.noarch. 30 MB/s | 155 kB 00:00 (54/61): python3-rpm-generators-13-3.fc37.noarc 7.4 MB/s | 29 kB 00:00 (55/61): python3-rpm-macros-3.11-6.fc37.noarch. 3.8 MB/s | 14 kB 00:00 (56/61): python3-setuptools-62.6.0-3.fc37.noarc 48 MB/s | 1.6 MB 00:00 (57/61): python3-urllib3+socks-1.26.18-1.fc37.n 4.0 MB/s | 9.6 kB 00:00 (58/61): python3-urllib3-1.26.18-1.fc37.noarch. 33 MB/s | 258 kB 00:00 (59/61): xz-devel-5.4.1-1.fc37.x86_64.rpm 17 MB/s | 65 kB 00:00 (60/61): python3-libs-3.11.6-1.fc37.x86_64.rpm 54 MB/s | 9.6 MB 00:00 (61/61): gcc-12.3.1-1.fc37.x86_64.rpm 57 MB/s | 33 MB 00:00 -------------------------------------------------------------------------------- Total 74 MB/s | 90 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.11-6.fc37.noarch 1/61 Installing : fonts-filesystem-1:2.0.5-9.fc37.noarch 2/61 Installing : python3-rpm-macros-3.11-6.fc37.noarch 3/61 Installing : libmpc-1.2.1-5.fc37.x86_64 4/61 Installing : cpp-12.3.1-1.fc37.x86_64 5/61 Installing : pyproject-rpm-macros-1.10.0-1.fc37.noarch 6/61 Installing : fontawesome-fonts-1:4.7.0-14.fc37.noarch 7/61 Installing : google-roboto-slab-fonts-1.100263-0.18.20150923git 8/61 Installing : lato-fonts-2.015-14.fc37.noarch 9/61 Installing : python-setuptools-wheel-62.6.0-3.fc37.noarch 10/61 Installing : python-pip-wheel-22.2.2-3.fc37.noarch 11/61 Installing : kernel-headers-6.5.4-100.fc37.x86_64 12/61 Installing : glibc-headers-x86-2.36-14.fc37.noarch 13/61 Installing : libxcrypt-devel-4.4.36-1.fc37.x86_64 14/61 Installing : glibc-devel-2.36-14.fc37.x86_64 15/61 Installing : expat-2.5.0-1.fc37.x86_64 16/61 Installing : annobin-docs-12.28-1.fc37.noarch 17/61 Installing : mpdecimal-2.5.1-4.fc37.x86_64 18/61 Installing : libtool-ltdl-2.4.7-2.fc37.x86_64 19/61 Installing : libb2-0.98.1-7.fc37.x86_64 20/61 Installing : python3-3.11.6-1.fc37.x86_64 21/61 Installing : python3-libs-3.11.6-1.fc37.x86_64 22/61 Installing : python3-docutils-0.18.1-2.fc37.noarch 23/61 Installing : python3-idna-3.3-4.fc37.noarch 24/61 Installing : python3-charset-normalizer-2.1.0-2.fc37.noarch 25/61 Installing : python3-imagesize-1.2.0-9.fc37.noarch 26/61 Installing : python3-markupsafe-2.1.1-3.fc37.x86_64 27/61 Installing : python3-jinja2-3.0.3-5.fc37.noarch 28/61 Installing : python3-pygments-2.12.0-4.fc37.noarch 29/61 Installing : python3-pyparsing-3.0.9-2.fc37.noarch 30/61 Installing : python3-packaging-21.3-6.fc37.noarch 31/61 Installing : python3-rpm-generators-13-3.fc37.noarch 32/61 Installing : python3-pysocks-1.7.1-15.fc37.noarch 33/61 Installing : python3-six-1.16.0-8.fc37.noarch 34/61 Installing : python3-urllib3+socks-1.26.18-1.fc37.noarch 35/61 Installing : python3-urllib3-1.26.18-1.fc37.noarch 36/61 Installing : python3-requests-2.28.1-3.fc37.noarch 37/61 Installing : python3-snowballstemmer-2.2.0-2.fc37.noarch 38/61 Installing : python3-sphinx-theme-alabaster-0.7.12-16.fc37.noar 39/61 Installing : python3-sphinxcontrib-applehelp-1.0.2-10.fc37.noar 40/61 Installing : python3-sphinxcontrib-devhelp-1.0.2-10.fc37.noarch 41/61 Installing : python3-sphinxcontrib-htmlhelp-2.0.0-7.fc37.noarch 42/61 Installing : python3-sphinxcontrib-jsmath-1.0.1-18.fc37.noarch 43/61 Installing : python3-sphinxcontrib-qthelp-1.0.3-11.fc37.noarch 44/61 Installing : python3-sphinxcontrib-serializinghtml-1.1.5-6.fc37 45/61 Installing : python3-pytz-2023.3.post1-1.fc37.noarch 46/61 Installing : python3-setuptools-62.6.0-3.fc37.noarch 47/61 Installing : python3-babel-2.10.3-3.fc37.noarch 48/61 Installing : python3-sphinx-1:5.1.1-1.fc37.noarch 49/61 Installing : gc-8.0.6-4.fc37.x86_64 50/61 Installing : guile22-2.2.7-6.fc37.x86_64 51/61 Installing : make-1:4.3-11.fc37.x86_64 52/61 Installing : gcc-12.3.1-1.fc37.x86_64 53/61 Running scriptlet: gcc-12.3.1-1.fc37.x86_64 53/61 Installing : annobin-plugin-gcc-12.28-1.fc37.x86_64 54/61 Running scriptlet: annobin-plugin-gcc-12.28-1.fc37.x86_64 54/61 Installing : gcc-plugin-annobin-12.3.1-1.fc37.x86_64 55/61 Installing : python3-sphinx_rtd_theme-1.0.0-8.fc37.noarch 56/61 Installing : python3-devel-3.11.6-1.fc37.x86_64 57/61 Installing : python3-Cython-0.29.32-2.fc37.x86_64 58/61 Installing : xz-devel-5.4.1-1.fc37.x86_64 59/61 Installing : zlib-devel-1.2.12-5.fc37.x86_64 60/61 Installing : bzip2-devel-1.0.8-12.fc37.x86_64 61/61 Running scriptlet: bzip2-devel-1.0.8-12.fc37.x86_64 61/61 Verifying : python3-sphinx-1:5.1.1-1.fc37.noarch 1/61 Verifying : bzip2-devel-1.0.8-12.fc37.x86_64 2/61 Verifying : fontawesome-fonts-1:4.7.0-14.fc37.noarch 3/61 Verifying : fonts-filesystem-1:2.0.5-9.fc37.noarch 4/61 Verifying : gc-8.0.6-4.fc37.x86_64 5/61 Verifying : google-roboto-slab-fonts-1.100263-0.18.20150923git 6/61 Verifying : guile22-2.2.7-6.fc37.x86_64 7/61 Verifying : lato-fonts-2.015-14.fc37.noarch 8/61 Verifying : libb2-0.98.1-7.fc37.x86_64 9/61 Verifying : libmpc-1.2.1-5.fc37.x86_64 10/61 Verifying : libtool-ltdl-2.4.7-2.fc37.x86_64 11/61 Verifying : make-1:4.3-11.fc37.x86_64 12/61 Verifying : mpdecimal-2.5.1-4.fc37.x86_64 13/61 Verifying : python3-babel-2.10.3-3.fc37.noarch 14/61 Verifying : python3-charset-normalizer-2.1.0-2.fc37.noarch 15/61 Verifying : python3-docutils-0.18.1-2.fc37.noarch 16/61 Verifying : python3-idna-3.3-4.fc37.noarch 17/61 Verifying : python3-imagesize-1.2.0-9.fc37.noarch 18/61 Verifying : python3-jinja2-3.0.3-5.fc37.noarch 19/61 Verifying : python3-markupsafe-2.1.1-3.fc37.x86_64 20/61 Verifying : python3-packaging-21.3-6.fc37.noarch 21/61 Verifying : python3-pygments-2.12.0-4.fc37.noarch 22/61 Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 23/61 Verifying : python3-pysocks-1.7.1-15.fc37.noarch 24/61 Verifying : python3-six-1.16.0-8.fc37.noarch 25/61 Verifying : python3-snowballstemmer-2.2.0-2.fc37.noarch 26/61 Verifying : python3-sphinx-theme-alabaster-0.7.12-16.fc37.noar 27/61 Verifying : python3-sphinx_rtd_theme-1.0.0-8.fc37.noarch 28/61 Verifying : python3-sphinxcontrib-applehelp-1.0.2-10.fc37.noar 29/61 Verifying : python3-sphinxcontrib-devhelp-1.0.2-10.fc37.noarch 30/61 Verifying : python3-sphinxcontrib-htmlhelp-2.0.0-7.fc37.noarch 31/61 Verifying : python3-sphinxcontrib-jsmath-1.0.1-18.fc37.noarch 32/61 Verifying : python3-sphinxcontrib-qthelp-1.0.3-11.fc37.noarch 33/61 Verifying : python3-sphinxcontrib-serializinghtml-1.1.5-6.fc37 34/61 Verifying : zlib-devel-1.2.12-5.fc37.x86_64 35/61 Verifying : annobin-docs-12.28-1.fc37.noarch 36/61 Verifying : annobin-plugin-gcc-12.28-1.fc37.x86_64 37/61 Verifying : cpp-12.3.1-1.fc37.x86_64 38/61 Verifying : expat-2.5.0-1.fc37.x86_64 39/61 Verifying : gcc-12.3.1-1.fc37.x86_64 40/61 Verifying : gcc-plugin-annobin-12.3.1-1.fc37.x86_64 41/61 Verifying : glibc-devel-2.36-14.fc37.x86_64 42/61 Verifying : glibc-headers-x86-2.36-14.fc37.noarch 43/61 Verifying : kernel-headers-6.5.4-100.fc37.x86_64 44/61 Verifying : libxcrypt-devel-4.4.36-1.fc37.x86_64 45/61 Verifying : pyproject-rpm-macros-1.10.0-1.fc37.noarch 46/61 Verifying : python-pip-wheel-22.2.2-3.fc37.noarch 47/61 Verifying : python-rpm-macros-3.11-6.fc37.noarch 48/61 Verifying : python-setuptools-wheel-62.6.0-3.fc37.noarch 49/61 Verifying : python3-3.11.6-1.fc37.x86_64 50/61 Verifying : python3-Cython-0.29.32-2.fc37.x86_64 51/61 Verifying : python3-devel-3.11.6-1.fc37.x86_64 52/61 Verifying : python3-libs-3.11.6-1.fc37.x86_64 53/61 Verifying : python3-pytz-2023.3.post1-1.fc37.noarch 54/61 Verifying : python3-requests-2.28.1-3.fc37.noarch 55/61 Verifying : python3-rpm-generators-13-3.fc37.noarch 56/61 Verifying : python3-rpm-macros-3.11-6.fc37.noarch 57/61 Verifying : python3-setuptools-62.6.0-3.fc37.noarch 58/61 Verifying : python3-urllib3+socks-1.26.18-1.fc37.noarch 59/61 Verifying : python3-urllib3-1.26.18-1.fc37.noarch 60/61 Verifying : xz-devel-5.4.1-1.fc37.x86_64 61/61 Installed: annobin-docs-12.28-1.fc37.noarch annobin-plugin-gcc-12.28-1.fc37.x86_64 bzip2-devel-1.0.8-12.fc37.x86_64 cpp-12.3.1-1.fc37.x86_64 expat-2.5.0-1.fc37.x86_64 fontawesome-fonts-1:4.7.0-14.fc37.noarch fonts-filesystem-1:2.0.5-9.fc37.noarch gc-8.0.6-4.fc37.x86_64 gcc-12.3.1-1.fc37.x86_64 gcc-plugin-annobin-12.3.1-1.fc37.x86_64 glibc-devel-2.36-14.fc37.x86_64 glibc-headers-x86-2.36-14.fc37.noarch google-roboto-slab-fonts-1.100263-0.18.20150923git.fc37.noarch guile22-2.2.7-6.fc37.x86_64 kernel-headers-6.5.4-100.fc37.x86_64 lato-fonts-2.015-14.fc37.noarch libb2-0.98.1-7.fc37.x86_64 libmpc-1.2.1-5.fc37.x86_64 libtool-ltdl-2.4.7-2.fc37.x86_64 libxcrypt-devel-4.4.36-1.fc37.x86_64 make-1:4.3-11.fc37.x86_64 mpdecimal-2.5.1-4.fc37.x86_64 pyproject-rpm-macros-1.10.0-1.fc37.noarch python-pip-wheel-22.2.2-3.fc37.noarch python-rpm-macros-3.11-6.fc37.noarch python-setuptools-wheel-62.6.0-3.fc37.noarch python3-3.11.6-1.fc37.x86_64 python3-Cython-0.29.32-2.fc37.x86_64 python3-babel-2.10.3-3.fc37.noarch python3-charset-normalizer-2.1.0-2.fc37.noarch python3-devel-3.11.6-1.fc37.x86_64 python3-docutils-0.18.1-2.fc37.noarch python3-idna-3.3-4.fc37.noarch python3-imagesize-1.2.0-9.fc37.noarch python3-jinja2-3.0.3-5.fc37.noarch python3-libs-3.11.6-1.fc37.x86_64 python3-markupsafe-2.1.1-3.fc37.x86_64 python3-packaging-21.3-6.fc37.noarch python3-pygments-2.12.0-4.fc37.noarch python3-pyparsing-3.0.9-2.fc37.noarch python3-pysocks-1.7.1-15.fc37.noarch python3-pytz-2023.3.post1-1.fc37.noarch python3-requests-2.28.1-3.fc37.noarch python3-rpm-generators-13-3.fc37.noarch python3-rpm-macros-3.11-6.fc37.noarch python3-setuptools-62.6.0-3.fc37.noarch python3-six-1.16.0-8.fc37.noarch python3-snowballstemmer-2.2.0-2.fc37.noarch python3-sphinx-1:5.1.1-1.fc37.noarch python3-sphinx-theme-alabaster-0.7.12-16.fc37.noarch python3-sphinx_rtd_theme-1.0.0-8.fc37.noarch python3-sphinxcontrib-applehelp-1.0.2-10.fc37.noarch python3-sphinxcontrib-devhelp-1.0.2-10.fc37.noarch python3-sphinxcontrib-htmlhelp-2.0.0-7.fc37.noarch python3-sphinxcontrib-jsmath-1.0.1-18.fc37.noarch python3-sphinxcontrib-qthelp-1.0.3-11.fc37.noarch python3-sphinxcontrib-serializinghtml-1.1.5-6.fc37.noarch python3-urllib3-1.26.18-1.fc37.noarch python3-urllib3+socks-1.26.18-1.fc37.noarch xz-devel-5.4.1-1.fc37.x86_64 zlib-devel-1.2.12-5.fc37.x86_64 Complete! Finish: build setup for python-pysam-0.22.0-1.fc37.src.rpm Start: rpmbuild python-pysam-0.22.0-1.fc37.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1699920000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.LYFUgg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcvcf.c pysam/libcutils.c pysam/libctabixproxies.c pysam/libctabix.c pysam/libcsamtools.c pysam/libcsamfile.c pysam/libchtslib.c pysam/libcfaidx.c pysam/libcbgzf.c pysam/libcbcftools.c pysam/libcbcf.c pysam/libcalignmentfile.c pysam/libcalignedsegment.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.SUnJV6 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + 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-0.22.0 + FORCE_CYTHON=1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + 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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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-311 creating build/lib.linux-x86_64-cpython-311/pysam copying pysam/config.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/version.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/utils.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-311/pysam creating build/lib.linux-x86_64-cpython-311/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-cpython-311/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) 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 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.htslib.cram' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.cram' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.htslib.cram' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.htslib.cram' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.htslib.htscodecs.htscodecs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.htslib.htscodecs.htscodecs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.htslib.m4' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.m4' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.htslib.m4' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.htslib.m4' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.htslib.os' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.os' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.htslib.os' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.htslib.os' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.samtools.lz4' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.samtools.lz4' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.samtools.lz4' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/py.typed -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/version.h -> build/lib.linux-x86_64-cpython-311/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-311/pysam creating build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/README -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools creating build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-x86_64-cpython-311/pysam/include/samtools creating build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/README -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-cpython-311/pysam/include/bcftools creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/README -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/configure -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/header.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/region.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4 creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib creating build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c cythoning pysam/libcutils.pyx to pysam/libcutils.c cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2579:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2584:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2628:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2633:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c 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. cythoning pysam/libctabix.pyx to pysam/libctabix.c cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c cythoning pysam/libcbcf.pyx to pysam/libcbcf.c cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code 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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/pysam gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/htslib_util.o build/temp.linux-x86_64-cpython-311/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-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-x86_64-cpython-311/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-311/samtools creating build/temp.linux-x86_64-cpython-311/samtools/lz4 gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/amplicon_stats.c.pysam.c:39: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/amplicon_stats.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam2depth.c.pysam.c:37: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam2depth.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_addrprg.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_addrprg.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_ampliconclip.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_ampliconclip.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_aux.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_aux.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_cat.c.pysam.c:39: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_cat.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_color.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_color.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_consensus.c.pysam.c:128: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_consensus.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_fastq.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_fastq.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_flags.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_flags.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_import.c.pysam.c:36: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_import.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_index.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_index.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_lpileup.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_lpileup.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_markdup.c.pysam.c:32: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_markdup.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_mate.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_mate.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_md.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_md.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_plbuf.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_plbuf.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_plcmd.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_plcmd.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_quickcheck.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_quickcheck.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_reheader.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_reheader.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_rmdup.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_rmdup.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_rmdupse.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_rmdupse.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_samples.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_samples.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_sort.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_sort.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_split.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_split.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_stat.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_stat.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bamshuf.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bamshuf.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bamtk.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bamtk.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bedcov.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bedcov.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bedidx.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bedidx.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/consensus_pileup.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/consensus_pileup.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/coverage.c.pysam.c:36: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/coverage.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/cram_size.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/cram_size.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/cram_size.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/cut_target.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/cut_target.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/dict.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/dict.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/faidx.c.pysam.c:34: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/faidx.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/padding.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/padding.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/phase.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/phase.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/reference.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/reference.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/reset.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/reset.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/reset.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_opts.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_opts.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_utils.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_utils.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_view.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_view.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sample.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sample.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/stats.c.pysam.c:42: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/stats.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/stats_isize.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/stats_isize.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/tmp_file.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined 158 | #define _XOPEN_SOURCE 600 | In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/tmp_file.c.pysam.c:1: /usr/include/features.h:214: note: this is the location of the previous definition 214 | # define _XOPEN_SOURCE 700 | gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-311/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-311/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-cpython-311/bcftools gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 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-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 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-I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS 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-I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS 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-Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic 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-fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong 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-I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-cpython-311/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-0.22.0/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.22.0/htslib/htslib/hts.h:37, from /builddir/build/BUILD/pysam-0.22.0/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/gff.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/version.c.pysam.o build/temp.linux-x86_64-cpython-311/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcbcftools.cpython-311-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:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ building 'pysam.libcutils' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-x86_64-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcutils.o build/temp.linux-x86_64-cpython-311/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcsamtools.cpython-311-x86_64-linux-gnu -lcbcftools.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcutils.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28594:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28594 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:14277:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14277 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libctabix.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-x86_64-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:67308:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67308 | (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_4__dealloc__’: pysam/libcbcf.c:67033:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67033 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:72167:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72167 | (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:35331:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35331 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35357:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35357 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcbcf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-311/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 -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-x86_64-cpython-311/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.constprop.0’: pysam/libcvcf.c:25769:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25769 | __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:20201:10: note: ‘__pyx_v_qual’ was declared here 20201 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-cpython-311/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -Lbuild/lib.linux-x86_64-cpython-311/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.22.0/build/lib.linux-x86_64-cpython-311 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.0/build/lib.linux-x86_64-cpython-311 + sphinx-build-3 doc html Running Sphinx v5.1.1 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/3.11/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.11/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.11/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 building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] api reading sources... [ 22%] benchmarking reading sources... [ 33%] developer reading sources... [ 44%] faq reading sources... [ 55%] glossary reading sources... [ 66%] index reading sources... [ 77%] installation reading sources... [ 88%] release reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 11%] api writing output... [ 22%] benchmarking writing output... [ 33%] developer writing output... [ 44%] faq writing output... [ 55%] glossary writing output... [ 66%] index writing output... [ 77%] installation writing output... [ 88%] release writing output... [100%] usage generating indices... genindex done writing additional pages... search done copying static files... done copying extra files... 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.qASEV3 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + 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-0.22.0 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + 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-0.22.0-1.fc37.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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/version.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/config.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/samtools.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/Pileup.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/utils.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/__pycache__/__init__.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-311/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcf.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabix.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcutils.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcftools.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/os creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-311/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/gff.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-311/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-311/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include copying build/lib.linux-x86_64-cpython-311/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam copying build/lib.linux-x86_64-cpython-311/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/bcftools.py to bcftools.cpython-311.pyc writing byte-compilation script '/tmp/tmpts8xmn0n.py' /usr/bin/python3 /tmp/tmpts8xmn0n.py removing /tmp/tmpts8xmn0n.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 package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) 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 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam-0.22.0-py3.11.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.22.0-1.fc37 --unique-debug-suffix -0.22.0-1.fc37.x86_64 --unique-debug-src-base python-pysam-0.22.0-1.fc37.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.22.0 extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbcftools.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbcf.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libctabix.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcutils.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11/site-packages/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so original debug info size: 24696kB, size after compression: 23300kB /usr/bin/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. 43594 blocks + /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/python3.11/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.11/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.11/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.11/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib/debug/usr/lib64/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/lib64/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.22.0-1.fc37.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hG0Ucp + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python3-pysam + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python3-pysam + cp -pr README.rst /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.YBIxNc + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam + cp -pr COPYING /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam + cp -pr bcftools/LICENSE htslib/LICENSE samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam cp: will not overwrite just-created '/builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam/LICENSE' with 'htslib/LICENSE' cp: will not overwrite just-created '/builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/licenses/python3-pysam/LICENSE' with 'samtools/LICENSE' + : + 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-311-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-311-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-311-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-311-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-311-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-311-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-311-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-311-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-311-x86_64-linux-gnu.so()(64bit) libctabix.cpython-311-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-311-x86_64-linux-gnu.so()(64bit) libcutils.cpython-311-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-311-x86_64-linux-gnu.so()(64bit) python-pysam = 0.22.0-1.fc37 python3-pysam = 0.22.0-1.fc37 python3-pysam(x86-64) = 0.22.0-1.fc37 python3.11-pysam = 0.22.0-1.fc37 python3.11dist(pysam) = 0.22 python3dist(pysam) = 0.22 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_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-311-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-311-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-311-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) = 3.11 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.0-1.fc37 Processing files: python3-pysam-devel-0.22.0-1.fc37.x86_64 Provides: python-pysam-devel = 0.22.0-1.fc37 python3-pysam-devel = 0.22.0-1.fc37 python3-pysam-devel(x86-64) = 0.22.0-1.fc37 python3.11-pysam-devel = 0.22.0-1.fc37 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) = 3.11 Processing files: python-pysam-doc-0.22.0-1.fc37.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xDRil7 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python-pysam-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python-pysam-doc + cp -pr html /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.0-1.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.0-1.fc37.x86_64 Provides: python-pysam-debugsource = 0.22.0-1.fc37 python-pysam-debugsource(x86-64) = 0.22.0-1.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.0-1.fc37.x86_64 Provides: debuginfo(build-id) = 070ee8f7bb761668ff3e3d4d169515bffa078574 debuginfo(build-id) = 0be399c4fc63d43fcb9ae00c71434efd50b1871c debuginfo(build-id) = 0fa7f1c318eb124bdbc73c7357685c27dd3df03a debuginfo(build-id) = 114d0eeabf0d9d42b5d760a75f70006362e8edd8 debuginfo(build-id) = 11a81a06af45f32c1972dbb80bd49142f8f86c92 debuginfo(build-id) = 14759674ca605c6e5e331d47e1961d7501e8a500 debuginfo(build-id) = 486e80ea7d597faf8bf8075169c3769ad4b2fe1f debuginfo(build-id) = 4cc931a8fa710fdfdb598d5d0aeca7c03d7b7a56 debuginfo(build-id) = 92f9af08e08ee5b27f835d24dbaeb8d6ad0c3443 debuginfo(build-id) = a4125780b49c934fbd36264630d07b7f4db96d7a debuginfo(build-id) = bf3b0aba4dccff353b4e262d3d7b2cbb177730b2 debuginfo(build-id) = cd3ec92d909de0d18ff81f8f07053b108b212791 debuginfo(build-id) = e3b0b1a2635d7b9269ae77c870056bbdd9a48dd1 libcalignedsegment.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcalignmentfile.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcbcf.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcbcftools.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcbgzf.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcfaidx.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libchtslib.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcsamfile.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcsamtools.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libctabix.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libctabixproxies.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcutils.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) libcvcf.cpython-311-x86_64-linux-gnu.so-0.22.0-1.fc37.x86_64.debug()(64bit) python-pysam-debuginfo = 0.22.0-1.fc37 python3-pysam-debuginfo = 0.22.0-1.fc37 python3-pysam-debuginfo(x86-64) = 0.22.0-1.fc37 python3.11-pysam-debuginfo = 0.22.0-1.fc37 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) = 0.22.0-1.fc37 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 Wrote: /builddir/build/RPMS/python3-pysam-0.22.0-1.fc37.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.0-1.fc37.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.0-1.fc37.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.0-1.fc37.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.0-1.fc37.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.tjHkcg + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-1.fc37.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.LShSLw + umask 022 + cd /builddir/build/BUILD + rm -rf pysam-0.22.0 pysam-0.22.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: File listed twice: /usr/share/licenses/python3-pysam/LICENSE File listed twice: /usr/share/licenses/python3-pysam/LICENSE Finish: rpmbuild python-pysam-0.22.0-1.fc37.src.rpm Finish: build phase for python-pysam-0.22.0-1.fc37.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.rpm.log /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.librepo.log /var/lib/mock/fedora-37-x86_64-1699922217.139082/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.22.0-1.fc37.src.rpm) Config(child) 3 minutes 32 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-doc", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "noarch" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "x86_64" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "x86_64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "src" }, { "name": "python3-pysam-devel", "epoch": null, "version": "0.22.0", "release": "1.fc37", "arch": "x86_64" } ] } RPMResults finished